Ok, an update. Not sure what's going on, but the system somehow seems to be completely ignoring anything over 1Ghz. I'm not sure how my phone was rebooting last night, but I haven't been able to make it happen even setting ridiculous frequencies. Even setCPU is showing the higher frequencies that are being set. Benchmarks are showing that the clocks aren't going over 1Ghz, though. With a ton of digging, I've found that even with the frequency tables set for overclocking and the max frequency set to an overclock, /sys/devices/system/cpu/cpu0/cpufreq/cpuinfo_cur_freq never goes over 1000000. /sys/devices/system/cpu/cpu0/scaling_cur_freq also shows the same. I really have no idea how they have this locked down right now, especially with even setCPU showing the overclocked frequency (even scaling up and down from it).
More to come as I continue to dig. If anyone else has any input as to what might be locking this down, please do share. This exact method works just fine on the Droid 1 and Milestone even on the stock kernel.