I had that problem recently, only my loops were smaller than yours. My troubleshooting research said the loops were caused when the stitch length and the manual movement of the FMQ were not in agreement. I was on a basting stitch (5), but I was FMQ'g too slowly to accommodate the long stitch. So I switched to a smaller stitch (3) and moved at the same speed and no loops.
Since I like the longer stitch, I FMQ'd quicker and that solved my problem. Might be worth a try if you're still having a problem.