Help - Couverture on truffles is cracking.

Yesterday I made a batch of truffles and the couverture that I coated them in (53% valrhona) cracked on 50% of them. It happened after they were set and I left them out at room temperature to set. This has never happened to me before and I cant think of a reason why it would have happened. Anyone else have this problem before or any ideas why it would have happened?
updated by @valerie: 04/20/15 10:10:14PM

Too cold filling?

Nope, they were at room temperature. I got interrupted while making them so I covered them with plastic wrap and came back about 2 hours later to temper the chocolate and dip them.

There were three types - raspberry ganache, caramel ganache and whiskey ganache. They were all rolled to a round shape. I'm not familiar with the term bottomed (but curious, would love to know the process). I thought the chocolate was tempered perfectly and it did take around 7 minutes to set. The finished truffles have a nice sheen and color, but cracks on half...

You might want to do a hand coat first-put a dollop of tempered chocolate into your hand and roll the truffle around in it. Let the chocolate set. This first thin coat will strengthen the second coat and prevent cracking. Then dip your truffles again.To bottom, use a stencil with tempered chocolate to form bottoms (aka chablons, see http://www.shopchefrubber.com/home.php?cat=1540 ), then pipe your filling on top, let set, and dip.