Presser foot height will definitely affect your stitches. For example, if you were using a machine that was equipped with a floating foot (like the Westalee ruler foot for domestic machines) and it was just a little too high above the quilt surface, then the result would be skipped stitches, that's because a foot that is too high will allow the fabric to "flag" or come up with the needle, which then prevents the stitch from forming properly. The same thing can happen with a Hopping foot--- so even if the thread tension at the top and bobbin are correctly balanced, you may need to adjust the presser foot pressure knob to get it at the correct height. Check the height when the presser foot is at its lowest point in the stitch cycle. On a very thin quilt sandwich, you may need to increase the presser foot pressure (which will effectively lower the height of the presser foot slightly). I didn't realize the Juki sit down had that adjustment-- very handy. On my Sweet Sixteen I have to use a wrench to manually screw the foot in higher or lower to adjust it.
Hope that helps,
Rob