Got an updated server or server software?

Restart Thunderbird with add-ons disabled (Thunderbird Safe Mode). On the Help menu, click on "Restart with Add-ons Disabled". If Thunderbird works like normal, there is an Add-on or Theme interfering with normal operations. You will need to re-enable add-ons one at a time until you locate the offender.

Tried it, it's not working.

I recently updated thunderbird, this is around the time this started happening. I usually don't update, so I'm not sure how old my version was. Definitely haven't updated in the last six months

I'm using IMAP with GoDaddy mail by the way. I understand it's a common issue, but I've never had it before until two weeks ago, around the time I updated.

LawnSigns said

I recently started having this issue after an update and moving my profile around....

Why did you move the profile around, or more importantly: did you remove (or failed to copy) the .msf files OR chose to "Repair" some folders in the Properties dialog? I’m not entirely sure, but these flags might get stored in there, so removing or not copying the files could have removed the flags. You could probably pinpoint this by sending another reply.

I also recall a few questions with regard to GoDaddy and specific issues with starring messages (they would be added for Preferred senders) that may be of help - see here and here.

I've moved my profile because I switched to a new computer. Going back to the old computer, the same issue appeared.

All the .msf files seem to be there. I completely copied the profile folders in the local and the roaming folders for Thunderbird appdata.

The issue is that the stars get removed after I star a new message when I select a different letter to read. Same thing with the arrows which indicate I've replied to a mail. Also, read mail gets marked as unread when I move the selection cursor to a different email. This is really causing me trouble keeping up which people I've replied to, and I fear that when business picks up I'm going to start losing clients :(

I've downloaded and installed an older version of Thunderbird (45.1, released around May 2016) and it didn't really do anything.

lets go back... a star is not always a star.

This is a new mail with the unseen flag set.

Thfollowing is a mail with the unseen, unread and star all set.

The last on the line is the star. The first as I said is the unseen and the green middle one is the unread.

Can you confirm you really mean Star? I do know clicking on the unseen Asterisk does mark the message read and remove it and clicking on the star does not (at least on my device.)