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Possible Duplicate:
Binding of Isaac achievements and Steam in-game not working
I defeated Mom for the first time, but I did not get the Killed Mom! achievement on Steam.
I played as Magdalene and had some neat accessories:
Did I not get the achievement because of Magdalene or her items?
I will assume that you do not have a problem getting achievements in general (otherwise, you should indeed try the solution proposed here), but that you failed to obtain the specific achievement you are asking about.
Having played quite a bit of this game myself, there have been several cases where an achievement did not unlock for me when it should have (though as far as I remember these were always "Unlock item XXX" achievements, such as The Spelunker). Luckily, the game seems to take the fact that it has issues unlocking achievements into account, and I've always had said achievements unlock the next time I started up the game.
That being said, your achievement may still not unlock, so know that you did nothing to disqualify yourself from obtaining it (I don't think there's any actual way to do that. You get it even if you take the easy way out and kill mom using The Bible. Heck, you even get an extra achievement for that). Since killing mom is something you do quite often in the game, you'll probably get this achievement soon enough one way or another, though that doesn't make the fact it did not unlock properly any less annoying.
To reduce the chance of achievement unlocking issues in the future, you can still check out this thread mentioned in the answer I pointed to earlier. I'll admit I never did try the fix from that thread, personally, as I did not need it.
