It is very important to use only bobbins meant for Janome. On the 6600, the bobbin must be flat on both sides - no concave whatsoever. My bobbin used to jump around until I changed out to ones meant for Janome. SOnce doing so, I have had no problems. I buy them on E-bay from a gal who sells them by the bag in different quantities. Last time I bought 50 and this next time, I will do the same. I keep at least 5 of the top colors I use filled at all times.
Also, you must hold the bobbin and top threads back and to the right of the needle when you start out stitching otherwise the threads can get all 'nested up' underneath.
When all else fails, rethread everything, clean out your bobbun area, make sure the needle screw and the foot screw are tight. Good luck!