Thunderbird is not able to save the file when closing. That may be due to an antivirus or other software interrupting the save. The problem may also be due to the large size of the file. My suggestion is to move a large percentage to Local Folders. I would then review the inboxes, as the one with highest number is probably the current one. Once verified, you could delete (with thunderbird not running) the other files and rename the highest-numbered one to Inbox. Also, check to see if there are multiple copies of prefs.js. If there is just one, then the inbox problem is most probably due to the size alone.