I had a similar problem until I activated encryption and disabled legacy clients that didn't enable that. I think my ISP was using packet filtering/shaping to slow my connection whenever they detected BT traffic.
My vote is for uTorrent as well. It offers encryption.
i use Azureus, and the only thing i need to do is to put a limit to the UPLOAD speed, i put a maximum of 50% of it and i have no problems
the download speed doesn't matter, i've played starcraft with 3 friends while i use Azureus downloading at 50 kbs and uploading at 7.5 kbs (my conection is of 1 MB) and NO lag
i can download crap from a webpage with 0-10% download speed loss at the same time too