Originally Posted by Ingy
When you do your next water change vacuum the sand really well. That's not normally something you do but you may have lots of dead aerobic bacteria still decaying in the sand. Suck em out. Personally i would even remove the under filter completely as I keeps a dead space of water under there. Your other bacteria should be doing fine if you're only having nitrate probs.
Excellent advice. I agree 100%.
OP, your power filter and skimmer are not causing this. They are both part of the long term solution. People abandoned using undergravel filters because they are highly prone to pitfalls. Believe all of us who have had years of success with saltwater aquariums. None of us would ever use one and our tanks are much better without it. Infinitely so. With a little work your tank will be fine.