The recent cfitsio version region filtering fails when the first region is an exclude. This was an error I introduced when extending to multiple components as allowed in the FITS REGION extension. The fix should be available next week. Meanwhile a work-around is to include an initial region covering the entire field.
Update 12/15/08: There is also a memory-handling error in the code which reads a FITS REGION. This bug is only triggered if the extension contains a large number (>100) of exclude regions.