If you're trying to both GPU and CPU mine at the same time on Windows, not only will you want to keep one core free for GPU mining, you'll want to set the CPU miner to affinity of the other cores. For example:
start /low /affinity 0x0e minerd.exe --threads 3 ...
I have a four-core machine, so I create three threads, and affinity is set to cores 2, 3, 4 (i.e. 0x02 | 0x04 | 0x08 = 0x0e). You might also want to set the affinity of the GPU miner to the first core in a similar fashion.
By restricting GPU mining to core 1, and CPU mining to cores 2 and 3, I can get both 250 MH/s for BTC and 8.5 kH/s for LTC...