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Are you using a hopping foot or a floating foot to FMQ with?
If it's a floating foot, is it just barely touching the fabric? If it is too high, it can cause all kinds of trouble.
Sometimes my thread jumps out of the arm that goes up and down and then I get a mess, so check that your machine is threaded correctly. Also, at one point, when I first got mine, (I have the same model as the 6500), I was putting the thread where it is supposed to go when I fill a bobbin, instead of where it is supposed to go when I sew. So, check that.
Watson