I'm a lurker here, but an active poster over on RC. I've gone barebottom the past year with excellent results.
You have a phosphate problem. Test kits are not very helpful, if you can measure phosphate you have a huge problem.
You need to remove unmeasureable organic phosphate, get some serious rock cleaners going, and the live rock will "clean" itself. My Starboard tank is 6 months old and the rock is still spewing out crud.
Suggest a phosphate removing media such as Phos-ban, fluidized in a reactor. PO4 minus or Sailfert's phosphate killer is another option, or do both (I did). You'll see dramatic results as the phosphate falls. Be sure you have appropriate algae eaters, either fish or snails, have also heard good things about the "sea monsters" available at blowfishaquatics.com.
Refugiums are not needed, and actually usually won't survive, with a high flow, overskimmed, "clean" starboard reef.
Over on Reef Central, a Marine Biologist who goes by "Bomber" gives invaluable advice regarding barebottom setups.
HTH
John