Lorli,
tell us how you are doing......was your thread coming out of the take up lever? If so, thread it from left to right, rather than right to left....it does a little wrap around the lever and does not effect your stitching.....later models of Janome have a latch on the lever that keeps the thread in.......so Janome knows of this isusue.

When cleaning the 6600--remove the plate and also lift out the bobbin holder. Clean all the lint and fuzz out of the area and gently brush/wipe the bobbin holder. Put a drop or two of high quality sewing machine oil on the wick visible where the bobbin holder fits in. Replace the bobbin holder, matching the red dots. Screw down the plate. The machine should purr.

Also try turning the upper tension adjustment all the way left and all the way right, to make sure nothing is stuck. Then set at 4, or wherever you want it.

Just some ideas...