This problem is not related temperature.  It's related to physics, and understanding the behaviour of the chocolate you are working with.

When making chocolate confections, you have two compounds with different properties and different behaviours:  You have your centers, and you have your coatings.

As the centers warm and cool, they just sit there and for the most part, do nothing.  However it's important to keep in mind that some centers are softer than others, and also have more air incorporated into them than others, while other centers are dense, and less inclined to give in to slight compression.

Then you have your chocolate.  THIS IS THE CULPRIT.  As the cocoa butter in the chocolate crystalizes, it shrinks (which is why it comes out of molds very easily when properly tempered).  Chocolate with a high cocoa butter content (such as good quality couverture) shrinks LOTS, and when properly tempered, has zero maleability.

Your truffles are rolled round.

When a sphere shrinks, it shrinks inward.

You cover a round ball with tempered chocolate, and as the chocolate sets it tries to shrink.  However when it can't, something has to give, and as a result a crack appears.  It really IS that simple.

A very soft center with air incorporated into it (such as a whipped/piped ganache), will allow the chocolate to compress it and as a result will not crack.  A hard center will not give the chocolate an opportunity to shrink, and as a result many will crack.

Understanding the behaviour of your ingredients, you have a number of options:

1. Use a couverture that has less cocoa butter
2. Incorporate air into your centers by whipping them
3. Double dip your confections (the first dip will crack, but the second generally won't)
4. coat your truffles with something (which adds structure for the chocolate to grab on to and compress)
5. Use a milk chocolate to coat your confections

This lesson here is further supported by the process of molding chocolates.  The molds are poured, emptied, and scraped, and allowed to set before the filling is piped in (this gives the thin chocolate shell time to shrink).  The center is piped in, and the bottoms are poured.  Thick bottoms can cause cracking whereas uniform bottoms very seldom ever do.

Cheers and Happy Chocolate Making

Brad

like the other answers , the ganache is evidently too cold and, in my own experience, too soft. I have a rhubarb ganache that was really soft at room temperature so I froze it to be able to scoop it. I refroze the balls and dipped them in untempered chocolate as a first coat , the second,tempered, layer I did the following day having stored them at room temperature and one or two out of 50 bonbons cracked. I adjusted the ratio of chocolate to make it firmer and they no longer crack. I'm no physicist but the combination of freezing and lower viscosity seems to do it because I have soft filled molded pieces and they never crack or leak.... 

updated by @paul-john-kearins: 03/14/15 10:49:32

Here is some more food for thought.  In my experience, the more cocoa butter the dipping chocolate contains, the more prone to cracking with colder temps.  The Callabaut/Cocoa Barry suggested in the previous post I'm sure contains soy lecithin, which helps to counteract it a bit.  I use a lot of dark chocolate that doesn't contain soy lecithin, and it seems like the manufacturers use more cocoa butter to help emulsify.  When I started my biz, I read that ganache should never be chilled, and I've stuck to that train of thought.  The space I work out of is sometimes a bit of a challenge to keep warm during the winter, though, and if it is cool enough, some of my dark chocolate truffles will crack like crazy.  Hope this helps!

Did you ever solve your truffle cracking issue? I had the same problem. Check the fluidity of your couverture. Callabaut/Cacao Barry rates their couverture with droplets on the front of the package. I was using a "3" fluidity when the cracking occurred. Try using a couverture that is more fluid. Get a "5" if you can.

Sounds like you have a problem with your center temperature, I agree with what Jonathan recommended.

Try letting your ganache sit at in the molds are room temperature for 4-12 hours ('overnight') prior to chilling.

I find that the ganache needs to 'set up' and this happens while warm.

-Jon

So I've read just about every internet site that I can, and I've tried just about everything, but my truffles just keep cracking. My method: My ganache is 12 oz. of chocolate to 1 cup of cream, and I really like the texture. I then use silicon molds to shape and portion the ganache balls. I freeze the molds with the ganache, then take the ganache balls out and let them rest in the refrigerator for at least 24 hours. Sometime in this time I roll them quickly by hand to eliminate the flat bottom. I then take them out of the refrigerator and let them sit at room temperature for at least 4 hours, then I dip them in chocolate tempered with a Rev. x3210 machine by chocovision. When I dip them, almost every truffle cracks. I have tried first hand-rolling the truffles with a small amount of tempered chocolate, then dipping them. They still cracked. Many even crack when double dipped! Any ideas/help?

Thanks!

updated by @trula-r: 04/10/15 09:42:21