Well, most users cannot start up from MBR. Perhaps there are later versions of the ROM that allow it in your case: I don't know why it worked for you. But if it's working, and you're OK with it, and don't mind that it's not a supported configuration, you can certainly go ahead with it.
The other issue, well, sounds like a problem with the drive or some low-level driver... hard to say. Might help to open the Console application before you put it to sleep to see if anything is output to it that might prove useful.
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--Dave Nanian
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