Feel like I'm talking to myself here, but I think I figured it out.
UPnP screws up shaping. By default, uTorrent uses UPnP to map its port.
I disabled the UPnP mapping in uTorrent, loaded up my Shaper rules again, and now my Torrent traffic goes into the correct queues. Thankfully the only other traffic I use UPnP for is game systems, so I can hard-assign the "qGamesDown" Queue to UPnPd and this should work out OK.
(I actually have a few other port mappings in there from a Windows Home Server, but they aren't used enough for me to be concerned that they're in the wrong queue.)
I'm still not 100% on how I can handle "bursting" downloads (i.e. Road Runner powerboost).
What I've done now:
qLANRoot (i.e. incoming traffic) - I changed the "Bandwidth" from 7000Kb to 100 (percent). I then turned on the "Upperlimit" service curve, and specified my values in there. (M1 = 10000Kb which is what I've read is the powerboost cap, d=16000 or 16 seconds, according to wikipedia, and M2=7000Kb, my "normal" download speed). I haven't yet played with speedtest to see if this will work though.