Ok, I am one who loves using invisible thread, but when I use it for appliqué, I use it in the bobbin too, and use a small needle(size 60). I do however, use regular thread in the bobbin and invisible on top when quilting without problems.
What needle size are you using? Could it be too big? When it does sew, does the tension look right? I don't know much about your machine (or sewing), but surely if I can get it to work you could. I generally have to lower the top tension a bit, but never have problems with skipped stitches.
Sorry I can't me more of a help.