Network problems after installing server 2003 SP1

Hi,
I'm having some weird problems with my entire network, that i can't seem to
isolate. They started after SP1 was loaded on one of our DC's. Here is a
brief overview of our network

forest
_____________|____________
| |
domain 1 domain 2
| |
7 x DC's 1 x dc (exchange 2003 sp2) w2k3 sp1
1 x GC 1 x gc
NO SP1


Exchange (domain 2) points to domain 1 for GC access, user authentication.
all users are in domain 1

The problems started after DC1 (gc holder, dc1 does not hold any fsmo roles)
in domain1 was upgraded to SP1.
SP1 was then removed but the problems remained.
shutting down dc1 cured the problems.
bring dc1 back online re-introduced the problems.

the gc was then moved to DC2 in domain 1 (dc 2 has never had sp1 applied) to
keep exchange running.
shutting down dc1 did not cure the problems.
shutting down dc2 did not cure the problems.
shutting down both dc1 and dc2 does not cure the problem

GC moved back to dc1
shutting down dc1 did not cure the problems
shutting down dc2 did not cure the problems
shutting down both dc1 and dc2 does not cure the problem


The problems i am having are with users logging in. login scripts are set at
the user object, NOT applied by GPO. The script will run for a few lines and
then quit before mapping any drives.
Another problem is running software on workstations. For example :

PC1 with package 1 and package 2.
User 1 logs on, cannot run package 1 but can run package 2
User 2 logs on, can run both package1 and 2
User 3 logs on, connot run either package 1 or 2

All 3 users are members of the same groups, in the same ou, and were created
at the same time.

These problems only occured after SP1 was deployed to DC1.

I have tried calling microsoft, but all they can suggest is change the
scripts, and they run - problem solved! wrong answer microsoft.

Does anybody have any ideas, or has anybody seen this before?

Thanks in advance.
Paul Kelly