Look up the "nice" command.
Any CPU mining, whether built in to a coin or using minerd aka cpuminer or whatever, use "nice coind" or "nice minerd", it runs at lower priority so does not seem to impact GPU mining nor FPGA mining nor ASIC mining yet still gets to use most of the cores most of the time.
-MarkM-
For debug purpose, I've shut down my GPU mining and tried all cores. I still only get about 1200PPS in linux vm but I'm getting 6000 in Windows.
I was chitchatting with someone else and he said his Linux PPS got halved when he switched to this client too.
Which Linux distribution are you using? I suspect some distributions might not be supplying a properly optimized version of GMP. I may eventually start releasing my own Linux binaries.
Ubuntu 12.04
Looks like Ubuntu 12.04 comes with GMP version 5.0.2. That's from Aug 2011. It may fail to recognize newer CPUs. In that case, it won't choose the optimal code path.