Ok my two cents:
Often when you're quilting, skipped stitches are a result of needle flex. The thicker sandwich and added tension due to pushing/pulling the sandwich can cause the needle to bend slightly, and therefore miss the bobbin hook. The fix is to use a larger needle. When sewing on my DSM (Brother 1500), I usually use a 12 or 14 for piecing, but when quilting I got better results and no skipped stitches once I switched to a 16 or 18 needle. By the way - a size 18 is pretty standard for most longarm machines.