Contents of all messages in Inbox get deleted randomly - but fortunately not contents of subfolders.
At random intervals - weeks apart - Thunderbird suddenly deletes all the contents of messages in my Inbox. The message headers remain - until I 'repair' the folder when the messages disappear completely. Messages in subfolders are OK.
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How many messages do you keep in your Inbox? The article here advises that the best way to minimise this problem is to keep it almost empty: http://kb.mozillazine.org/Keep_it_working_%28Thunderbird%29
I only keep ~10 messages in the Inbox - and the problem doesn't seem to be sensitive to the number of messages
pop account or imap? which AV software are you running?
POP account Antivirus is AVG (Free version)