Do they itch?
Yes they itch a lot. I can't help but rub my fingers on them to alleviate the urge to use nails as I know that scratching it will cause it to scar and redden.
It could possibly be a fungus in that case - take a look at this thread for it. http://www.acne.org/...ld-be-a-fungus/
Otherwise, if it is simply closed comedones and congestion, I second trying to go back on a retinoid. Retin-a in gel form or retin-a micro would be better than the cream, as the cream has a pore clogging ingredient in it. I'm personally on differin gel, though.