I just hit 10k on stack-overflow, and I noticed that my rep graph ends up at what looks like just over 9000 (cough).
That's quite a mismatch. I hear there are problems with bounty rep not being counted, but I don't think I've ever set or won a bounty.
I'm not sure what the cause could be.. but perhaps someone could look into it.
Here's a screenshot of what I'm on about: