Hi Jim,
Either the mineral oil or the silicone mentioned by others will make
the shells look better after the fact.
Regarding the cause of the problem, there are a couple of
possibilities.  First, if you boil a good number of specimens
together in a relatively small amount of water, and don't rinse them
thoroughly, they may be coated with a residue of organic matter from
the "soup".  If that's the case, a short exposure to bleach (about 5
minutes) should remove it.
The problem could also be caused by water quality.  Tap water in most
localities is fairly alkaline, and will have no deliterious effects on
shells, but if you live in an area where the tap water is nearly
neutral in pH, and especially if it is on the down side (acid side)
of neutral, it could cause problems, especially if the shells are not
cooked promptly, and acids of decomposition are added to the mix.
Also, such effects are greatly increased as the temperature rises.
An effect that might take a few days to develop at room temperature
could occur in minutes in a boiling solution.  You would only notice
such effects on a smooth shell like a cowrie, olive, or Polinices
duplicatus.
If you live in an area where the water is very hard, it is possible
that the dissolved mineral salts in the water might react with the
shell, either precipitating on its surface, or replacing some of the
calcium.  Again, this sort of reaction would be greatly accelerated
by heating.
Finally, what sort of container are you boiling the shells in?  The
ideal vessel is one made of glass, either pyrex or kimax, or one of
the stove-safe glass materials like Corningware.  Stainless steel is
probably ok too, but I would stay away from aluminum or iron
containers.
Regards,
Paul M.