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cories with red gills

Tim mentioned his cories had red gills.  I don't know the number of fish, how
many were in each bag, the tank size or if they were struggling to breathe,
listless etc but here is a shot in the dark...

Sounds like it could possibly be ammonia burn.  In general, staying in the bag
for 45 minutes would not be enough time for them to generate that much ammonia
(unless the LFS tank was loaded and that doesn't sound like the case since
they were fine there).  You didn't mention how many were in the bag or how
much water was in it.   A bunch of fish and a little bit of water is a bad
combination because ammonia will build up quickly.    Losing color temporarily
is a stress reaction.  My guess is either your tank is experiencing an ammonia
spike possibly (newly set up and/or something has gone terribly wrong in tank
OR you had way too many fish with too little water for the ride home)  If it
were some other reaction to water (pH shock, temperature shock, etc.  they
would have a different reaction)

In general, when I have a fish problem the first thing I do is observe, the
second is check my water parameters (in this case, your ammonia levels)  and
third I do a water change.

Hope this helps or at least sparks something that helps you figure it out.

Good luck.