I'm going to be a little radical and say it could also be the foot you're using for the FMQ. I have a "big foot" for one of my machines and it causes skipping like crazy. If I change absolutely nothing else about the machine other than the foot and stitch I skip no stitches ever. The reason it skips is that it hangs up on the machine and doesn't hold the fabric right so the stitch can finish forming right. I'll fix it one day maybe.
Does the machine skip stitches at all if you stitch with it regularly? If not, look at the foot, your speed and coordination like has been mentioned and I bet you find the problem.
wendig - what did the LAer say about the skipped stitches? there are a LOT of factors on her end that could have caused the problem too.