^^ The Education Resource CD. That thing was awesome, always repaired all the funky issues with my Edu-OS 9.x Macs. Boot Driver is a good point, but is always installed if necessary by Disk Utility since OS 9.
Same with the Firmware, there were no Firmware updates for the eMacs because they booted OS X out of the box. Firmware updates were mainly for OS 9 - OS X boxes. All of the models you listed are dual-booting models, and thus required that update.
Incompatible boot records will cause the issue you're referring to. The boot record is empty or does not contain the correct pointer information, during the low-level format (aka, disk zeroing) that information is deleted. Open Firmware will dynamically reassign to the OS that's available on the drive when it detects a fresh drive. Hence why I suggested Option booting to see if the drive is available with an OS X icon. Sometimes that's all it takes. Couldn't have hurt to do an NVRAM flash to erase pre-existing system parameters as well.
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