I've had that problem ever since realdrums came out over a year ago, and mentioned it on this forum. I was hoping it would be fixed with the 2009 version, but no such luck. The only response I got was that I was not using the correct tempo for the part, which was not true.

I think the problem is that sometimes the loop points don't overlap correctly, and that results in the double kick.

I pull the drum part into an audio editor now after it is rendered and fix it that way, it's the only way to do it as far as I know.