I helped a few small company in administrating their PC. To prevent the user from installing software and to prevent from infection of computer virus, I have set their accounts to limited account.
However some legacy software installed on the protected area of the drive (EG. C:\legacy_program) and require write access might have problem for these limited account to run the program.
A quick search I did on the Internet found this article which mentioned the workaround to this, is to use access control list (ACL). To do this, you can use the GUI to configure or by the following command:
cacls "C:\legacy_program" /e /t /p users:c
If this still doesn’t help, it could be the case that the legacy program is trying to write to registry as well. You will need to locate the registry and configure the necessary permission.