When I was setting up my bike with a cheap Nashbar tensioner in push down operation I had bad skipping under hard pedaling. As best as I could figure, eventough the chainline was fine the frame would actually flex slightly causing the downward hanging tensioner to feed the narrower link plates on to the top of the teeth of the rear cog. About half way around they would drop back in and cause a skip. I added a half link, took out a full link, and removed the spring and rigged my tensioner with a wire tie to push up on the chain. No more problems.
Anyway, I'm sure you have your chain as short as possible, but could a half-link allow you shorten it slightly further?
Also if your tensioner is pushing down it may help to make it pull up for more chain wrap.