I have a 6600P also. I have no advice to offer on the thread cutter. Sorry. But on the automatic threader, I learned that the needle has to be in right position (I always push the needle up button to be sure); and the threader has to be all the way down. Then make sure you put the thread in front of the needle (it's easy to get it behind the needle). It's not a perfect system, but it works. I will say that the threader for my Janome 350e embroidery machine is a lot easier to use than the one on the 6600.
I agree that you need to try it before you leave the repair shop. Good luck.