I found a fix for this problem.. On this thread there is a ini file that I used to replaced my corrupt one. After loggin in I got everything (all windows and filters) how I like them, then logged out, and when I logged back in everything was retained. All font sizes and windows where good. The only hassle is having to get everything set back up the first time, but it's worth it in the longrun.
Thread to fix this problem. It's post #5