This problem could be two-fold. The most likely strongest culprit is, indeed, moisture. Refridgerators are very humid animals and even more so if they are especially filled, where the air circulation is impeded.
I make probably 150 or so various truffles. And I prefer to first store them in the freezer (much less humidity), but I go an even further step or two: First, I use well-sealed plastic "Tupperware-type" tubs and line the bottom with several sheets of paper towels. Then the truffles are place in layers with waxed paper as the base. A final layer of waxed paper goes on top of the final layer of truffles, then a few more sheets of paper towels, then sealed very well. To thaw, I remove the container from the freezer, wrap the thing in many layers of plastic wrap and leave the container in the refrigerator for 24 hours.
If I'm having a short turnaround between making and giving, I will store them in the refridgerator by the same method as above, sealing the final container with lots of plastic.
Kyles, an obvious truffle pro, does the same thing I do with cocoa-coated truffles by storing the truffles within lots of extra cocoa. A good shake and they're gorgeous.
However, I suspect another equally strong culprit is the alcohol in your ganache, which will tend to dissolve the cocoa, in my experience. For any liquor-based truffle or cream, for this reason, I always dip those into tempered chocolate.
I find basic truffles are easily coated in cocoa, but again, anything with alcohol should be coated in tempered chocolate.
