New skimmer tend to have a break-in period where they will produce microbubbles for a couple of weeks. You could also check to see how many bubbles are being created as water enters the sump. You may need to implement a some type of homemade diffuser to help control the bubbles on the intake side. How many over-under sets baffles do you have?
New systems tend to have microbubble issues. If all else fails, give it a while and it should settle down a bit on its own too.