koala

Go to Tools > Message Filters, highlight one of the filters and click the Edit button. Under 'Perform these actions', are any of them set to 'Mark as read' in the first box?

I've looked at all the options in Tools > Options and Tools > Account Settings and can't find anything else that would fix this problem.

The closest thing I can find is under Tools > Account Settings > Server Settings. If you put a checkmark in 'Fetch headers only' then it won't download the full message automatically, just the To, From and Subject details. You would then have to click 'Download the rest of this message' for each email, but it might prevent the message being marked as read.

This doesn't seem like an ideal solution though, even if it works. I only have 2 accounts in Thunderbird and no filtering to different folders, so hang on for a reply from other Thunderbird users if this doesn't fix it.