It can happen that your TB theme (unintentionally and therefore inadvertently) changes and as a result it doesn’t match with your custom css (in chrome folder). You can see below an example of this:
As you can see, you get not only a very ugly appearance, but using TB becomes almost impossible.
To fix this problem you have to check (in edit -> settings -> add-ons and themes) what theme you are using, and if necessary, re-set the correct one, that suits to your css.