David,
Have there been any variations in your freezing of the specimen?  The only
time I've seen
blatant staining inconsistency is when there has been problems with the
freezing of the
muscle.  (Sometimes the isopentane hasn't cooled enough, the muscle not
being dry enough,
etc.)  I've seen this happen when someone new starts in the lab and they
don't realize the
importance of following the protocol exactly.  One of my old bosses used to
flip out when the
clinicians didn't give us fair warning about a muscle biopsy.  He swore the
enzymes were
compromised because we were busy and didn't devote the proper time to the
freezing.
Beth Morehead
Med U of SC

P.S.
(Dr. Jimmy Powers, if you're out there...YOU know what I meant....."former"
NOT "old"!!)