What weight is the thread that is causing the knots? If it is thicker--try a larger needle. My guess is that it is a short staple thread and your other thread is a long staple so it's not really knotted--just fuzzier. You can run several lines of sewer's aid down the cone or spool or spray the with silicone lubricant. It will act as a de-frizzer which will keep the auto-tensioner on your machine from freaking out.