If you have a parallel connection between the CPU and GPU blocks, disconnect the CPU block, put caps on its feeds and run the pump (use an external 12V source or disconnect everything from the PSU and use the PSU + paperclip to run the pump) to send all the flow through the GPU block. If there are bubbles in there, that should purge them.
Another possibility would be an obstruction in the GPU block.
If your blocks are setup in series, then both the GPU and CPU should be getting the same flow.
BTW, when you say that your CPU is staying below 40C, is that while running a burn-in test or idle? Idle temperatures are largely meaningless. If that was idle, run AIDA64, Prime95, SuperPi or anything else of the sort. If CPU temperatures shoot up, you have no flow through the CPU block either.