I have 2 Janomes and FMQ on them all the time. No problems. I have had to change the bobbin tension. I like to use Bottom Line in the bobbin. That is very fine, so, of course I had to tweek the bobbin tension. I'm not afraid of doing that. The old, "Don't EVER change the bobbin tension", was from the SMG who didn't want to have to deal with it. Not only that, but back then, we only had one kind of thread, usually Coat and Clark. Think of all the different thread out there now. Yes, we do have to help our machines know the difference sometimes. If you use to completely opposite colors in top and bottom - I don't think that there is a machine out there that can stitch and not have the bottom show through to the top.
Just keep trying different things and don't give up on your Janomes. I love mine.