I am using Mathematica 8. I know this is old, but …
It seems that when I have a bug, and Mathematica goes off producing a long string of error messages, the Abort Evaluation (alt-.) does not work. My only alternative is to use Task Manager to kill the kernel.
I’ve had similar trouble in the past. In my case, my buggy program generated error messages much faster than the Front End can load and format them in a notebook. While the Front End is busy doing that, it doesn’t read & process the ALT-. input until all the messages that have been queued have been printed — or so I’ve inferred. Then in prints all the messages that have been generated in the meantime.