User Agent: Mozilla/5.0 (Windows NT 6.1; WOW64; rv:30.0) Gecko/20100101 Firefox/30.0 (Beta/Release) Build ID: 20140605174243 Steps to reproduce: 1) Start Thunderbird (TB) upon booting PC (Windows 7 Home Premium). 2) Exit TB. 3) Attempt to start TB later. 4) Message appears that it is already running, and that I need to re-boot to get TB back up. Actual results: Started Windows Task Manager. TB was NOT in the Applications list as implied by the error message above, but rather showed up on the Process list twice. Deleted TB from Process list by using "End Process" command for each appearance in the list. Then able to restart TB. Reinstalled TB version 24.0.1 to cure the problem after several vain re-boots and tries to get v 31.0 to work properly. This seems similar to Firefox Bug 541016 on your list. Expected results: TB should restart after being closed without re-booting the computer or resorting to manual removal from the Windows Task Manager process list. That is how 24.0.1 works.
So Thunderbird is in the startup list or startup folder? I don't know if it uses startup folder in safe mode, but please try safe mode and tell us what happens. https://support.mozilla.org/en-US/kb/safe-mode