I think the main problem is running the chiller at full capacity or past it. Might be a psu problem so check that first. If you have psu running at full capacity there are minor tweaks you can make. I would then setup a water temp monitor to help troubleshoot. If nothing works, with two dual 120mm rads you should get great temps.
PH did a review on the chiller. He got very cold coolant temps at higher flow rates but didn't change cpu temps that much.
http://www.procooling.com/index.php?...s&disp=84&pg=2
The review shows flow rates on the cold side is important and higher flow rates meant lower temps. I think with the sli setup, 10mm tubing and 450lph 1.8M x2o pump means you are having very low flow rates. You can get better performance with bigger tubing on cold and hot side and a bigger pump on coldside loop.
He concluded insulatation was a possible propblem since he didn't insulate the cpu block. Did you insulate the apogee and gfx cards in dieletric grease then enclosed in foam? The foam is a key component and the grease alone isn't enough. Due to their large surface area, if you don't insulate the two cards properly you will have a second pathway that will transfer the heat.