Was trying to figure out why running the cpuinfo script from Android Terminal, it would only show current cpu frequency speed at 599.xx today. I checked it for awhile, it wouldn't ever display what it should have been at 799.xx.
This is a Droid 1, running 0.4 with chevyNo1 lv 0.8, since it came out.
Ran a couple tests to see if it was just a problem with the terminal, but it is indeed not applying the 800mhz like it always has. I had made a backup a few days ago, so I restored that, and it was showing at 799. again. Updated a few apps, rebooted and checked again - normal.
Installed the Droid2 live wallpaper, and switched the Droid X boot animation to the Droid2 boot animation I got on droid-life.com with the switchboot script. Rebooted and checked, all good still.
Then I downloaded and applied the stopOTA update.zip again, and went through RM to boot into recovery and install it again as I had the frist time. Then checked cpuinfo. And it was again at 599.xx mhz.
I had made a copy of the build.prop file before I did this, and so I overwrote the new build.prop to the old one, rebooted and it's back to 799.xx.
I had also tried the fixperm script the first time I noticed this. Gave me some error, (can't recall) but it didn't apply itself either. So not positive but other scripts might have been broken by it too.
Also not sure if it may be having a possible conflict with the specific chevy kernel or not, but I did install the newest chevy lv 0.8 froyo kernel to see if that would fix it the first time, and it didn't. I have been using the slightly older chevy froyo lv 0.8 kernel all the time I've been using 0.4 without any problems.
I dont use SetCPU, I just use the overclock script Pete puts in the ROM.
Not saying it breaks it for everyone else, just saying it does for my setup.