Just to make sure we are all talking about the same setting in BOINC Manager it is "On multiprocessor systems, use at most 99 % of the processors.

I'm guessing that it only looks like it is the CPU usage percent that effecting your 2x275 GPU crunching and is more likely the GPU driver being *green* and throttling itself down into 2D mode.

I leave Precision open to keep both cores of my old GTX295 in 3D mode. Do not use SWAN_SYNC for 2XX series.

I'm pretty sure SWAN_SYNC is only ever going to use one core in total but I don' have 2x4XX to test that out for you.
Suspend WCG fpr a minute and see what Task Manager has to say about it?

If you are using WCG to manage your profiles they give you an option of a number of cores instead of a percent.

Are you on the XS team? Do you crunch under another name on GPUGrid?