I have the same problem with my Brother CS-6000. I can change thread (bobbin and top) and use the same spool of thread, if I don't use from the same spool of thread even if it is the same brand, weight and color etc it will knot up.
I have wasted a lot of thread because of this. I have taken it all apart and cleaned it and it dosen't make any difference it still knots up.
It is very frustrating.