Sounds like there is a problem with the view of a specific group. Do the following:
1. Create a user account that has permissions to modify the view and modify the tree ( I think it is modify the tree )
2. Assign a template but do not assisgn any projects
3. Save the user account and then log into CM as the new user account
4. Working in each group, right click the All Projects folder or which ever the folder name is and Administer -> Modify View
5. When the view window opens with all of the projects in it, look to see if there are any projects on the same level as the root folder All Projects and take note of their name(s)
( If there are any, select a project that is within a sub folder or off of the root folder and move it and then save the changes )
6. Close out of the view window and then right click All Projects -> Administer -> Modify View
7. Add the projects back in that appeared on the root level
You will need to check each view that is in each group database. There is another way to get the list of projects and the group database they reside in by running a query against the group database but I do not remember how to do that.
You should now be able to log into CM as any admin user and not get the INTERNAL SERVER ERROR. If this is the case, then you received that message because you had rights to see the problem project while other users may not have permissions to see the problem project(s).
Hope this helps.