From MozillaZine Knowledge Base
This article documents some common problems installing Thunderbird 3.0 that were discussed in the forums. It doesn't attempt to duplicate the release notes. See Thunderbird 2.0 installation issues if you run into a older issue such as: Error opening file for writing: nmozMapi32.dll. Click Retry to try again, or Cancel to stop the installation
If you are using the Lightning calendar add-on you need to upgrade it for Thunderbird 3.0. Its available here. If you are using the Enigmail add-on update to the most recent version to avoid crashes. Its available here.
You can run the migration assistant again using Help -> Migration Assistant if you change your mind about which toolbar to use etc..
- If you enable Global Search/Indexing information about every message in every account (except News) is stored in an SQLite database. This feature is still buggy, and the the index for global search requires substantial disk space. In v3.0 one person's testing shows an average of 3.5 KB needed per message . This can vary greatly depending upon the size and type of messages you receive. Some users have also reported that the size of the profile keeps growing even after it had enough time to index all of the messages. If it uses too many resources you can disable it in Tools -> Options -> Advanced -> General -> Advanced Configuration -> Enable Global Search and Indexer.
- If you can't update an add-on it will frequently work if you disable version checking per Updating add-ons. If it doesn't work correctly you can either disable or uninstall it (from Safe Mode if necessary).
- It is strongly recommended that you backup your profile before upgrading to 3.0. If you go back to 126.96.36.199:
- It may create a smart folder account (due to having used smart folders in 3.0) that gradually corrupts folder listings. You can't delete it except by editing prefs.js.
- Your passwords are stored in a different file in 3.0. However, the old passwords file is not deleted so if your passwords haven't changed you don't need to re-enter them again.
- If you switched to the new toolbar using the migration assistant you may have to customize the toolbar again.
- Your add-ons may have been upgraded to versions that are not backwards compatible if you enabled automatically checking for updates for add-ons.
- If you enabled Global searching/Indexing the global-messages-db.sqlite file in your profile is useless, and may waste a lot of space.
- The new Account Wizard is easier to use but can make some unusual choices such as using an IMAP server in the Gmail domain while using a SMTP server in the Googlemail domain. It might also pick an existing SMTP server from another account that uses a different username rather than creating a new SMTP server entry. You can fix this by editing the account, the main thing is to be aware that these types of mistakes are being made. 
- Poor performance moving or deleting messages if you store your profile on a file share. It appears to be because they replaced some XPCOM calls with ones that don't do buffered writes.   .
- Password prompting is no longer sequential. Thunderbird may prompt for a password and while you are typing it display a prompt for another accounts password. The best workaround is to have the password manager remember them. 
- If you have problems recognizing the icons in the toolbar in the message pane install the Customize Header Toolbar add-on, right click on the toolbar and remove the junk and archive buttons. This will create enough space that it will display text next to the remaining icons.
- The Personas add-on is an extension, not a theme (like it is in Firefox). However, it doesn't work with all themes. 
- The account manager uses different terminology for secure connections. It uses "STARTTLS" for "TLS" and "TLS if available", and "SSL/TLS" for "SSL". 
- If you have connection problems check whether "use secure authentication" was enabled by the upgrade. It does that for gmx.com.  Its also possible your firewall wasn't smart enough to detect you upgraded Thunderbird and ask permission to apply the rules to the new bits.
- Thunderbird 3 has a session restore feature. This can have side effects such as it no longer remembering the last message when you start Thunderbird again, like it used to.  
- There is a modified version of the FolderPaneTools extension, which provides an option to select a default startup folder to be selected rather than the last folder before Thunderbird was closed .
- Folder names are now highlighted to indicate that they have new messages pending , the color depends on the desktop theme which may make it hard to recognize , . Follow the instructions here to change it with userChrome.css entires.
- You can individually change each folders settings and it will remember them. However, if you don't like the default settings there is no way to change it once for all folders. 
- The old version of the MoreFunctionsforAddressBook add-on can cause your address book to become unusable and you may lose mailing lists. Its recommended that you uninstall it before upgrading, and then install the version that supports 3.0. Look for it at the bottom of the extension's home page. 
- Thunderbird 3 supports plug-ins. However, unlike Firefox it doesn't support any settings to control what plug-ins get installed. For example if you have Google Chrome installed Thunderbird will install its Update plug-in. All that you can do is disable the plug-in. There is no official statement on what plug-ins are supported but the Java and Flash plug-ins work.
- Thunderbird adds a .eml file extension by default to attachments. If somebody complains that your messages get flagged as possible viruses due to the file extension you can disable that feature in Tools -> Options -> Composition -> General -> Forward Messages. 
- Addresses in the headers are replaced with "You" if they match any of your identities. If you don't like this you can disable it by unchecking "Show only display name for people in my address book" in Tools -> Options -> Advanced -> Reading & Display
- Auto-complete uses both the main and additional email address. 3.0 listed the additional address first in some cases. That is fixed in 3.0.4, it now alphabetically sorts them. . 
- Auto-complete didn't pick the most frequent address in 3.0. That was fixed in 3.0.3.  If you type comma-separated partial addresses, it does not auto-complete them when you press Tab or Return. That was supposed to be fixed in 3.0.2 but is still broken.  
IMAP specific (incoming mail)
- It checks for new mail in remote folders despite settings saying it shouldn't. 
- Setting a folder offline using the folder properties doesn't effect the folders in Synchronization & Storage -> "Keep messages for this account on this computer" (and vice versa). Pick one method and stick with it.
- Global indexing may index Gmails "All Mail" folder too, duplicating all of that accounts messages in the SQLite database.
- If you don't enable message synchronization you might run into a problem printing attachments if they can't be displayed inline. If this occurs you will see (Loading content for Printing) Preparing ... The simplest workaround is to view the message source using View -> Message Source (or Control-U), wait for it to load the entire message and then try again 
- If you get notified of new mail while dragging and dropping messages it cancels that operation and the folder you were hovering over gets stuck highlighted in blue 
- If you disable message synchronization you may run into some problems due to the entire message not being downloaded. For example, trying to print a message with an attachment. The workaround is to set mail.imap.mime_parts_on_demand false using the Config editor. The trade off is that whenever you read a message it will always fetch the entire message (including any attachments).
- You may want to set it false anyways if the disk cache is enabled. Thunderbird will not cache a message unless it has the entire message. 
- If a lot of read messages seem to be falsely marked as unread set mail.server.default.use_condstore false using Config editor. The setting disables an optional IMAP feature used to detect and resolve conflicts when multiple clients modify the same message. Unfortunately, disabling this feature will slow performance a lot in large folders. The bug seems to be fixed in the nightly builds for 3.0.2. 
SMTP specific (outgoing mail)
- Settings that have worked with 2.0 may no longer work with 3.0 after migration.
- If your server does not require any authentication, you will receive an error message referring to server authentification not used (SMTP-AUTH) . Thunderbird 3.0 now considers it an error if you specified "Use name and password" but the server doesn't request it (Thunderbird 2.0 silently ignored that setting).
- Similarly, if you have selected "Use secure authentication" (this setting was not available in 2.0 and just probed for), but the server doesn't support it, you will receive an error notification when trying to send the message. This option is probed and the checkbox may be set automatically when you are sending a message for the first time, also after migration from 2.0 .
- In this case, go into the Account Settings, last item "Outgoing Server (SMTP)", select the respective server, and click on Edit. Uncheck the box causing the problem. Note that it is unsafe to have "Use name and password" checked without either connection security or secure authentication selected!
- If you are running a 32 bit build on a 64-bit Debian or Ubuntu distribution (or one of their variants) a library problem might cause a connection problem. If this happens either set network.dns.disableIPv6 to "true" using the Config Editor or install the correct version of the lib32nss-mdns package.  
- New mail notifications on Mac OS X are integrated with Growl. However, it doesn't appear to support messages that are moved to a child folder by a filter 
- Thunderbird 3.0 can read the OSX system address book but any changes you make go to the Thunderbird address book. There is no support for writing the OSX system address book. 
64-bit build specific
- If you use a 64-bit Thunderbird build you can't use the Mozilla build of Lightning with it. The Calendar project only provides 32-bit builds. Get a 64-bit Lightning build from wherever you got that Thunderbird build. This problem typically occurs if you use a 64-bit Linux distro that provides a 3rd party build of Thunderbird in their repository. 
Useful forum threads