I complete guess, but uTorrent may be rate limiting ACK packets along with actual file transfer data. normally you can't do this because TCP ACK packets are handled by the OS, but many BitTorrent clients have a UDP based protocol called uTP and the "ACK" packets, quoted because they're logical ACKs not official ACKs, are handled by the program.
I don't use uTorrent anymore because of some major bugs and riddled with ads, but there was an option "Options -> Preferences -> Bandwidth -> untick 'Apply rate limit to transport overhead'" You could try unchecking this if it is checked. Otherwise you'd have to ask in their forums or wait to see if anyone where knows.