Repair Relationship issues

I have an issue with a module which has now been removed. However when ever i try to run a repair on the database I get a notification about having to repair relationships. When I do that, the same module that was removed comes up as causing a database failure. Could this be a SQL issue? Would the module and table need to be removed via SQL instead?
Any help or guidance in this regard will be appreciated.
Thanks in advance.

Delete following files and then Run Repair/Rebuild