Run multiple copies of Thunderbird at the same time
From MozillaZine Knowledge Base
Normally you can only run one copy (or instance) of Thunderbird at a time. If you try to launch a second copy, the second copy detects another copy is running and kills itself.
How Thunderbird usually behaves
If one copy of Thunderbird is running normally and you launch an additional copy of Thunderbird using a command line argument, what happens depends upon whether you're trying to have it start in the main window or in a child window. If you try to start a second copy of Thunderbird with a main window (a fully functional copy of Thunderbird) it detects another copy is running and kills itself. If you try to start it at a child window such as the address book or the compose message window it will create the window. For example, you can use thunderbird -addressbook to open Thunderbird's Address Book window. You can have as many copies of Thunderbird started in a child window as you want, even multiple copies of the same child window. The main limitation is only one copy of Thunderbird can support the main window.
Its possible a copy of Thunderbird is running even though you can't see any sign of it on the screen. This can occur due to an error when exiting Thunderbird where it closes all of its windows but the process is still running. When this occurs the only sign it exists is that its listed in the task manager and you have a problem launching Thunderbird (because it would be a second copy). The workaround is to stop the copy that is already running. For example, you could stop the Thunderbird process in the task manager, you could log out and log in again, or you could reboot your computer.
If you only need another Thunderbird window, then double-click a folder to open it in a new window. Alternatively, get a context menu for the folder and choose Open in New Mail Window from the context menu. For example, to work with an account in a separate window, double-click the account's Inbox folder.
Making Thunderbird behave differently
Multiple instances of Thunderbird can be launched by starting Thunderbird with a -no-remote command line argument or by setting the environmental variable MOZ_NO_REMOTE=1 before you run any copy of Thunderbird. You must use a different profile to run each copy of Thunderbird, so if profile manager does not normally appear during startup then you will also need to specify -P on the command line. Multiple instances is intended for debugging, so use it at your own risk. (-no-remote first appears in version 2.0 via bug 325509. For earlier versions you must use MOZ_NO_REMOTE=1.)
Some other customization possibilities are:
Thunderbird opens multiple times when started
This shouldn't happen, but regression bugs can cause that. The workaround is to close all copies of Thunderbird and delete the sessions.json file in the profile. Help -> Troubleshooting Information -> Show Folder will display your profile using Windows Explorer. 
New window by double clicking on folder
If you double click on a folder in the folder pane it will create another instance of Thunderbird if you're using a version before 2.0. Its possible to create many instances this way. This feature can be disabled using the No New Window On Double Click extension. That extension only supports 1.0+ so you need to use one of the methods in Updating add-ons to run it if you're running 1.5.*.
Double clicking is not working in 126.96.36.199, instead right click on a folder and select 'Open':- a new instance will open with the folder active in the new window.
Two MinimizeToTray Plus icons in system tray
If you notice that you have two MinimizeToTray Plus (or MinimizetoTray Revived) icons in your system tray when booting you have one instance of Thunderbird running despite the two "Thunderbird" windows. Usually it won't let you just close one of the windows when this happens. You can fix this problem by: