Yes this is more of a problem between uTorrent and the tracker sites. Bit Che is simply the middle man and is not responsible for mis-calculated peers.
I see this problem happen all the time even without Bit Che, the peers will never agree between the BT client and tracker. When it comes down to it, I think there are errors on BOTH sides. The tracker is obviously not updated as frequently as the BT client, so it will not reflect the most recent activity. Also, the BT client will often not find peers right away that are very distant, whereas the tracker is better capable of 'tracking' anybody (regardless of location).
With all this being said, it is simple a flaw in the BT system. Obviously what is most important is that your BT client finds the peers. To maximize this, you can enable things like DHT tracking and Peer Exchange in uTorrent. Also, make sure that uTorrent is properly configured with regards to port forwarding and # of connections, etc. For more help with setting up your client, I reference you to the uTorrent forums:
http://forum.utorrent.com/