I'm using the stock 2.1 which I rooted myself. I have busybox installed, su and superuser.apk. I definitely have root. Root apps prompt for permissions. However when I tried flashing an overclock kernel to flash_image, the device hangs at the Motorola logo boot screen. When I flash an overclock kernel .zip renamed "update" (such as bekit) applications lose root access, and I can't issue root commands in the terminal emulator, yet I can still be root through adb. This is obviously a problem, because even though I am clearly overclocked, I can't control it with SetCPU because it won't get root!
I am wiping data and doing advanced nandroid backups between each attempt. Currently, I'm using rooted, stock 2.1 with no overclock.
It's obviously something in the Bekit file, I just don't know what it could be. For the manual flash_image method, there must be something incompatible within the boot.img.
(PS - I'm not looking for a solution to overclock, but a little insight into this particular situation. I am well aware that I can flash a custom ROM.)