> Using clrmame 3.31 on win98se.

Get a real Operating system. 8)

> "used by a different program" message again for each problem set.

The message appears when some other task got access to the file which cmpro currently tries to work on. Possibly a not very good virusscanner, some other weird background tasks or maybe you got the set open in a zipprogram or similar.
Find the task which locks the files/folders, disable it and try again.

Roman Scherzer
ClrMamePro