That is odd, and I can't seem to replicate it. What version of Sonar are you using? How much controller data is there in each track, and is all controller information being sent on the proper channels?
Do you happen to be soloing tracks during this process at all? (The new Sonar versions have solo-dimming which reduces the other track volumes by 6-18dB)
If the difference is not super significant, another possibility is that your ear is selectively hearing certain parts.
6.2 PE is more than adequate, and nothing you've entered seems to be out of whack. Let us know how your experiments turn out.
If you're still experiencing the problem, would you mind sending me the CWP to take a look at? We can reduce it to possibly a hardware configuration or installation problem, or find a bug somewhere in KP2.