Some users have found a tagged message only shows the color when it's selected. The ReminderFox add-on is the culprit. Do you have it?

Don't know what reminder Fox add-on is all about. Only thing I do know. is that Fox and Thunderbird are both Mozilla products.

What exactly do you mean by 'stay highlighted'? After doing what?

Run TB in safe mode (hold Option when you launch TB). Any change with tags?

When I Tag (highlight) an e-mail all the letters turn to a color, lets say red and after closing the program and then reopen the Thunderbird app. it goes back to original color black.

As for TB have no idea what that means!

TB = Thunderbird.

Run TB in safe mode, tag a message, then restart again in safe mode, and see if the tag is still visible. Is the account POP or IMAP; check Server Type under Server Settings in Account Settings.

ranTB in safe mode, Tagged 3 messages then re opened TB. in Safe mode and all 3 messages remained tagged. Account is IMAP!

Next step is to disable all add-ons and see if the tags remain after restarting in normal mode. If they do, enable the add-ons one-by-one until you find the one(s) that make the tabs disappear on restart in normal mode. There are other possible causes, but this is the first diagnostic step.