Local System Account Broken

Can anyone give me any insight to this issue: I have been working on
troubleshooting it for 6 months now:

Out of 500 clients that use a specific program that requires a service to
run on the local machine with Local System Account - this has broken for
about 30 clients and I have tested moving into different OU and have removed
and rejoined to domain and renamed and rejoined to domain and have studied
RSOP on working clients and non working clients and find no difference. No
security filtering.

The program worked as long as a new service account was created with
priviledges to run this service but when I upgraded this package and
updgraded the clients, the clients will not work anymore at all and I feel it
goes back to this local service account breaking on these 30 users in the
first place.

Can someone tell me what I can check in the registry or the permissions of
the local service account and compare with non working users and working
users?

Tina