First off, make sure you have installed SP1 and the June Cumulative Update (both free downloads from MSDN).
Templates shouldn’t be attached to pools as their resources get added to teh pool workload. After saving a copy of teh template PMs should only then connect to teh pool, but preferably only after they have edited the schedule so resource usage matches what your resource managers/management/team leaders tell them what resource availability they can have. This avoids garbage data in!
Linking to resource pools is inherently risky. Every time anyone renames, moves or over-writes any linked file, the file corruption dice are rolled.
It is most likely that any problems are file corruptions so unlink all files, save as to new files then create a new, blank resource pool and re-attach project files.