I have an '05 X5 3.0i and it does the same thing with 52K miles. Not all the time, but once in a while. I've only had it happen when it's cold, driving the first mile or so.

I'll take my foot off the gas and coast down a hill, then when I give it some gas again, I get the little "bump" in the transmission. Nothing terrible, but it made me wonder also. Mine had the trans software update before I bought it in Sept 08.

If you ever figure out what's happening with your transmission, make sure you post back here. I'm guess lots of us have that issue.