I have seen some add ons cause this issue. You might try to restart Thunderbird with add ons disabled and see if things improve. You can do this from the Help menu.

I tried restarting with add on's disabled and it did not correct my issue. It's infuriating! This is my work email and I need to be able to know what I have and have not looked at! I think I will just be disabling Thunderbird if it continues to be an issue. I do not need to spend anymore work time trying to solve this problem. I have already went through all my settings many times looking for a way to fix it.

First, back up your profile, then right-click a folder, Properties, Repair Folder, and see if it makes any difference.

https://support.mozilla.org/en-US/kb/profiles-tb#w_backing-up-a-profile