I have a Janome Horizon, and have settled into the following setup for FMQ: blue bobbin case, tension at 3, feed dog tension at 5. I do best with Gutterman Dekor (polyester) thread in the top, and Bottom Line thread in the bobbin. I just recently did some work with metallic thread, which can be problematic, and it worked quite well ... better with a metallic needle
I had a lot of problems when I first got the machine last summer, but most were, I think, user issues.
Cotton threads don't work well for me.