Ok. I'm running SS 4.6 on my rooted Moto Droid using Chevy's uLv 1.1Ghz kernel. The CPU will not drop below 550Mhz at any point. The minimum set in SetCPU is 250Mhz, and the max is 1.1Ghz. It fluctuates, however, only between 550 and 1.1. I was originally running the uLv 1.2Ghz kernel and had no issues with that. This had started this morning from what I've noticed. I've tried re-flashing the kernel and re-installing SetCPU.
Any other ideas? I think my next step may be to try a low-voltage kernel.