Shake cpu usage woes since upgrading to Compressor 3

We used to render from the command line (shake 4.1) without a problem. When we sent something to render, all 4 cpus would be used to the max (near 400%). (we include the "-cpu 4" command)

Since upgrading to Compressor 3, it only works some of the time with no clear reason. Now I get less than 100% on a processor.

Very frustrating.

Any ideas on what makes it actually work when it does? Any work arounds?

I'm open to using q-master, but we haven't been able to get it to work in any reliable manner.