I have made a lot of truffles, and even more ganache for other purposes, and I have never had this happen. My guess is that you are boiling the cream too hard and that is causing the curdling.
How to make ganache:
You will need by weight one part 35% cream to 2 parts chocolate of your choice.
Chop your chocolate (if it's in blocks or chunks), put into a heatproof bowl (stainless steel is best) away fro your heat.
In a saucepan or pot (depending on how much you're making), bring the cream up to a high simmer.
Pour the cream immediately over the chocolate and stir with a silicone spatula if you have one, a wooden spoon otherwise. The chocolate should completely melt within about two minutes; longer for very high percentage dark chocolates. At this point if you are making flavoured truffles, add your flavourings (unless your flavour compounds have been infused into the cream).
Chill until set, make into truffles.
Edited to add:
If you are using alcohol as a flavouring in your truffles, you will need to use either more chocolate or less cream. I have found that approximately for every fluid ounce of alcohol added, remove 3/4-1 fluid ounce of cream from the recipe. I prefer to infuse flavourings in the cream, and have had great success with beets, bacon (with a Guinness reduction added to the chocolate later), black truffle and pureed walnut, and honey. Be sure to strain, of course, before adding the hot cream to the chocolate.
I have also found that white chocolate will often need slightly less cream than a milk or dark.
There are two things to keep in mind while melting chocolate:
Keep a low uniform heat
I start off the melting process with low to medium heat. Once the chocolate fully melts, I reduce the heat to low and keep gently stirring all the while.
If you allow the chocolate to cool, it separates out into non-uniform areas of heat, and the cooler pockets start crystallizing. This causes lumps or spikes to form. However, if you go too high, the chocolate may burn.
Keep the chocolate absolutely dry
This also includes steam and condensation from the boiler. The water in the boiler should not splash over or steam into the chocolate. Also make sure that the dipped materials (truffles in your case) are totally dry.
Presence of water causes rapid cooling of parts of the chocolate, which again causes lumps to form. It also causes sugar to crystallize out of the fine chocolate mix. This is called "seizing", and such chocolate is very brittle and difficult to melt.
EDIT:
Here's a nicely written article on the different methods of melting chocolate:
How to Melt Chocolate for Dipping
Best Answer
I don't know about perfectly round, but you can do better.
Stick toothpicks in the truffles before dipping. Dip them using the toothpick, let it drip enough to make sure there's not a ton of excess, probably while spinning it a bit to let it cool slightly and make sure it doesn't all accumulate in one place. Then stab the other end of the toothpick into something to hold it with the truffle at the top. (A block of foam works, as does cardboard, though you might need to pre-poke holes.)
This avoids having a lot of excess coating chocolate, which it looks like you're getting a lot of when scooping out with a spoon. There can still be a little excess, but it'll drip down the toothpick, not get smeared all over. It also avoids having to mess up any of the surface by touching it with the spoon.
Beyond that, they'll be as perfectly round as you managed to roll the centers, which is mostly just a matter of a bit of practice and obsessiveness. So they won't be perfectly round, but they'll be a lot smoother and rounder, definitely enough to impress people. You do get a small hole on one side of the truffle, possibly with a tiny bit of excess chocolate around it where it collected against the toothpick, but I don't think that's terribly ugly. Plus as long as a decent fraction are pretty, you can just eat your mistakes.
Here's what a friend and I managed on our first try:
As you can see, they're definitely not perfect. But we got better at it as we went along. A lot of the irregularities are from initial inexperience, variation in chocolate temperature (we didn't have a great water bath or hot plate setup), and simply not having terribly round centers.
Finally, you might want to practice tempering the chocolate a bit better. Having nice glossy smooth surface makes them look a lot cleaner even if they aren't perfect.