I have the same problem and I would just like people to know that I have fixed it.
It has nothing to do with Dr. Whatever and it is not the too many items glitch, as I have tested.
I don't know what causes the error, but I was able to fix it thanks to the post made by Scampi. When mine crashed, all I saw was a black screen and that there was an application error on falloutw.exe, but I couldn't get it drawn. I took the address on Scampi's post and did a little debugging. I didn't try to read what the address does, but I found a little jump over it so I reassembled it so that it hops over the call and I now have level 3!
Hope that helps.