I am using a 30 yr old mechanical machine so my answer is based on that machine.
When I fmq, I push the button to lower the feed dogs, and move the dial that controls the presser foot pressure to 'darn.' I use an open toe foot that seems to work really well for fmq. (A 'darning foot' is available, but mine broke and I didn't feel like stopping so I just put on a regular foot and it worked!)
My machine was doing the same thing and through experimentation, I discovered that though the 'darning' place on the dial was reccommended, it doesn't skip stitches when I increase the presser foot pressure just a bit.
I realize of course this may be something just my machine requires, but I thought I would add it here.
Hopefully by now you're problem is fixed.