I have the 6600 and I love it. I use any thread I want (including C&C). I would bet that it isn't threaded correctly. When I was at a quilt retreat a lady had a brand new 6600. She asked me to trouble shoot it for her. Figured out she had the bobbin in backwards. She didn't know that it was directional. She hadn't even noticed the drawing on the bobbin cover.
It is SO easy to miss a little detail and keep doing the same (wrong) thing over and over. I am sure your wife will love it once you get past this initial problem. I have had mine for 5 years now and it is a work horse that sews anything.
There is a yahoo group for the machine and they have files (and pictures) that are helpful. I agree the manual is not very helpful.
Good luck.
Mary