"Close to tray" addons are all broken
https://support.mozilla.org/en-US/questions/1229269 https://support.mozilla.org/en-US/questions/1189855
These keep being archived for some reason.
It is inexcusable that mozilla changed the plugin API without bothering to integrate even the most basic features that thunderbird RELIED ON ADDONS to do.
Chosen solution
FireTray for TB 60:
https://support.mozilla.org/en-US/questions/1242376
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I am unable to offer you any suggestions. Regardless of your opinions to the contrary. Add-on authors have always had the responsibility to make their add-on compatible, not the other way around.
You want the official reason, look in the bug report. https://bugzilla.mozilla.org/show_bug.cgi?id=208923
https://bugzilla.mozilla.org/show_bug.cgi?id=208923#c90 from 9 years ago
For Windows, as of Win7, Microsoft explicitly recommends *against* doing this:
"In this example from Windows Vista, Outlook and Windows Live™ Messenger are single-instance applications that minimize to notification area icons. ... Note: This icon pattern is no longer recommended for Windows 7. Use regular taskbar buttons instead if your program has desktop presence." [1]
Granted, Thunderbird currently doesn't have a lot of support for Windows 7 features (mostly because Gecko 1.9.1 doesn't support them either), but I think it would make more sense to put effort into Windows 7 support these days.
[1] http://msdn.microsoft.com/en-us/library/aa511448.aspx
You might also want to look at comment 132 in that bug where you get a link to a program that allows you to do what you want.
Personally I see no issue with the line Windows places under the running applications on my task bar. NO line not started, line running. So perhaps you need to consider placing your regularly used programs on the task bar to start with, instead of using it like in windows 3 as a place that only running applications appear.
Personally I see no reason I should go hunting to start Thunderbird, or Chrome or my other productivity programs. They are housed on the taskbar where they are accessible without leaving my current application to hunt around on the desktop or a menu.
Chosen Solution
FireTray for TB 60: