What you are describing is normal for a break in period. Since you skimmer is rather new, that is probably the issue. Just let it be and don't adjust it every time the foam head goes down. If you do, you will end up overflowing the skimmer. Once the skimmer has broken in, the skimmer will remain constant most of the time.
One more questions, what size of tank are you running the skimmer on?