I have a Janome 6600 and I had similar experience when I began using it. Exactly as you descibe in your free motion quilting. I took it to the shop and the repair man told me to
1) use an open toed free motion "foot"
2) always cut my thread before moving it to begin a new section
3) use "bottom line" thread (its thinner, stronger)
4) leave my feet up
And I've never had problems since (knock on wood)!
I even do my pre-quilting basting using my machine. A FEW pins in, 2" long stitches and I'm done in a matter of minutes (or a bit more if its a queen).
If all the advice you are getting here (and I guess on Yahoo also) doesn't work, get to a good shop (sometimes smaller ones aren't as knowledgable, and I suppose that may just be my experience -- but the ability to brain-storm can only help.
Frankly, I was having some rats-nests issue with my bobbin in regular sewing and since using the bottom line thread I've had no problems.... for about 2 years now. And NO, I don't know anyone from Superior company... I just followed my repairman's advice.
Good luck!