I think most folks on this forum tend to discount phosphate testing as useless; except for the purposes of selling stuff like phos-free. I'm no expert, so hopefully someone who knows more can weigh in. Personally, I'd shock with bleach just to see if you have something that you're fighting (even if you don't, you need to get chlorine in the pool while you're working through this problem). If you shock and you were fighting something, you'll probably have a nonzero CC level right after shocking. Also, if you are fighting something and you clear it out by shocking the swcg may then be able to keep up.

You should call pentair on the phone and ask them to help you troubleshoot. When I bought my house the swcg control board was bad and there was a diagnostic mode on it that tech support (in my case goldline/aquarite) used to accurately ID the problem based on the diagnostic numbers I read off to them from the control panel. Is the system still under warranty?