Most of the guys above have hit all the possible reasons.
#1 Replication may not be working, but since it was in the past it probably is ok, just turn off all of your BDCs leaving only the PDC running and see if the script works. If it does work replication is not working, fix that. Also note if the old script is still running when users logon replication is not working. I'd suggest making a dumby script that does something like this just to test replication functionality:
@echo logon scirpt is working properly.
pause
Then you will be able to determine if it is being run by all the workstations.
#2 The name of the script has changed and profiles have not been updated to reflect this change. save the old script and rename the new revised versio to the same name and location as the previous one.
#3 The script may not be writtin correctly. I'd suggest having it reviewed by a competent scriptor or posting it here. Some of us here, including myself are quite expert in thisarea.
Good luck.