It is more difficult to achieve all balanced stitch when FMQing because, as you move the quilt around in different directions, tensions change in subtle ways. I have a Bernina 1230 and -- although wonderful in every other way -- I have never been able to use two different colors of thread when FMQing. With mine, the problem is intermittent in that sometimes the bobbin thread shows on top and sometimes the top thread shows on the bottom. I am convinced that some machines simply cannot achieve and maintain perfectly balanced tensions when FMQing.
If you are working on a wallhanging, I would advise adjusting so that top thread shows on the underside; that way the top should be fine. If you are working on a quilt that will be washed, be aware that in the first washing this issue usually goes away what with changes in fabric and batting. The biggest problem would be in a show quilt when you do not want to wash the finished quilt before putting it on display.