If removing the profile is fixing the problem then a good candidate for the cause is the KiXtart group membership cache - have you been changing group names?

Add the "-f" flush parameter when you call the script to force the cache to refresh. Use todays date to avoid unnecessary refreshes.
 Code:
kix32.exe -f 2007/06/12 mylogonscript.kix


Try it on a login that you know is failing.

If that doesn't help, reduce your script to a few lines that demonstrate the problem and add some debugging output.