Ahhh the dreaded messing up of profiles that's encoded into the NT kernal of Windows 2000+.
By messing up are you saying the profile names are changing to 'DOMAIN.USERNAME'? If so, there is little you can do to stop this if you have already used the client under that username previously. This is because the NT core of 2000, XP and 2003 is rather specific when it comes to profiles and makes sure it does not generate problems for itself by trying to create profiles with exactly the same names as previously logged on users of (especially of seperate domains).
This is all on account of being able to enforce mandatory and roaming profiles, which means failsafe systems are in place to ensure original profiles aren't altered in any way.