Yuck. If you are getting prompted for files it could be due to your dllcache folder not being large enough. More likely you are simply finding mismatched files. Look in your event logs for Windows File Protection errors.
If being prompted for CDs is driving you nuts, create a slipstreamed i386 folder on your hard drive and point the SourcePath registry key to it:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Setup
You may also need to set CDInstall to 0. Can't remember, sorry.
If you suspect it's dllcache size, check this:
229656 Optimizing Windows File Protection Service
http://support.microsoft.com/?id=229656