When using a floating foot like the Janome fmq foot for ruler work, I've found that I need to sometimes adjust the height of the foot so it is just skimming or hovering slightly over the fabric. If it's too high off the fabric it can allow the fabric to move up some with the motion of the needle, that can cause stitch formation problems, particularly skipped stitches, it's possible that that could also contribute to thread breakage. Try using the thumb screw that is on the Janome foot to lower it a bit and see if that helps with the problem. You might also want to move to a larger needle when FMQ--Sometimes on my PQ1500s I've noticed that even if a needle seems to be correctly matched to the thread (thread the needle and see if it will easily slide along the thread) I still need to go to a larger size needle when FMQ--I think this has to do with the combination of thread and fabric.
I go back and forth between using my hopping foot and the Janome FMQ foot on my PQ1500s depending on what I'm doing. They each work better at some things than others for me.
Rob