I've been working for years now with Roaming Profiles but I have never heard of ntuser.dat files of this size ! Are you referring to the single ntuser.dat file or to the entire user profile folder ?
Btw, how long does it take for the user profile to load upon logon ???
What did you do to fix the prf-file? We are experiencing the same problem. ntuser.dat files grows to over 50Mb due to backup entries in the windows messaging subsystem key.