Check the database for tables that begin with VC_ . These tables house the cache information for the versioned objects. It is likely that at least one of these tables still contains data. Each of these cache tables can be cleared (purged) without loosing data that is in the project. Once cleared, the repair tool should be able to continue.

There is also a table called VersionControl that houses version control information also, and Defects can also be checked out, since you didn't mention those in the list of modules you have checked. As a side note I have seen before where entities were checked in but the VC tables referred to in the prior post also contained entries that weren't cleared when the check in was checked-in, reversed, or undone and clearing that table entry resolved the issue.