Hi twaltz,
Sorry to hear that you're having problems. I have a couple of questions for you that will undoubtedly help forum members to help you out on this one.
1.) When you say "3rd string", are you referring to the D string or G string? It's easy to mix these up.
2.) There are 3 different Guitar Fundamental courses, taught by 3 different instructors - Lisa, Anders and Chris. Which one are you currently undertaking?
3.) Which of your fingers has the deformity?
4.) Which barre chord form(s) are you having difficulty with (e.g. A minor, E minor)?
There are methods of stripping down certain barre chords that allow one to omit or mute some of the strings, so there's a good chance that there's a workaround that will work for you. Answering the above questions will help zero in on a specific solution. Thanks.
Sascha