I had been using No-Frills CPU control and IncrediControl. Switching to Trickster MOD did the trick.
I've proven that my cpufreq theory wasn't right, and after looking into it a bit more it might be that the ROM's mpdecision is overriding the defaults on boot. I'm installing kernel side mpdecision to see if that fixes it, but even if it doesn't it'll be a good feature to have. It'll allow more control of the kernel through Android Tuner.