Sounds like your problem is external to Moodle. If using LDAP, for example, you should be able to set up the groups such that your users are enrolled with student role rather than the custom role you have set up.
It may also be that you modified the student role rather than creating a new custom role for those instances where you need students to have more permissions. If that's the case, copy the student role, save it as a new role, then revert the original student role to defaults.
The first suggestion I made above would solve the problem in bulk, but would require you to do that manual process for each new course.