It's been a problem ever since realdrums came out. I first complained about it two years ago, and then also a year ago with the 2009 upgrade. And it happens exactly as you describe. I also know a lot about loops, been an acid user forever, and as you say the loops themselves are fine, the problem is they are not always assembled correctly and you end up with the double kick.

Very easy to see it if after you have rendered the track you then pull it into an audio editor, I'm using adobe audition here. And also very easy to fix after the fact in the audio editor, I just cut out the double kick out and replace it with a good kick, so for that reason it's not a huge deal for me.