Do you have multiple e-mail accounts set up in Thunderbird and perhaps used to use the extension Account Colors or some other extension that stoped working when upgrading your Thunderbird?

You can create custom tags using Manage Tags,
then use filters on each account to apply the tag to each account.

This colors messages from each account different colors.
Then you can if you want to also add color to the account folders.
Right click on a folder and chose Properties.
In the General information tab you can see Icon Color, change it to the same color you've added for the account tag.

Not ideal and as good as the old extension but at least it's solving the problem. :)