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I've had no trouble making Bart PE bootable flash drives before... though I haven't tried this method yet.

I remember moving HDDs with Win2K on them between machines used to cause a BSOD on boot IF you used non-standard HDD drivers that wrote the mainboard serial to the registry. The solution was move the HDD back to the original system, change to generic drivers and then you were free to move your HDD from system to system. I wonder is your problem anything like that?