They are Seagate Barracuda 7200.10 80GB HDs. They are the HDs my supplier said they sell as a HD for this model eMac so I would think they would work with no trouble.

Zeroing hard drives destroys all the data from front to back on the drive. It'll kill the boot records and create new blank ones, and remove recoverable bad sectors. (If they exist) It's pretty much a clean slate. So something on the drive was affecting the Disk Cloning process that's now gone.

Boot driver depending on the os system being installed on the do you know how new the os cd you are using is?? Dose it have the latest version of firmware information on it? Nothing wrong with zeroing out data best clean slate to work from removing anything that most manufactures have on the disk. The other question is the eMac firmware up to date???? This is important when making sure you are loading a fresh install.I know that eMac has a firmware update reset memory while using the power button.. Trust me sounds weird but it works. What I recommend doing is reading on every machine u upgrade on before installing any new hardware or software. This time you are lucky in that you where able to load software but some of the apple products that are out there is no repercussions to fixing things if upgrades are not performed without doing the firmware updates. perfect example, Quick silvers and some blue and white G3's and powerbooks. I know learned the hard way. Apple service source cd's if this is a school thing should be somewhere around the school or call there customer care. Apple usually will leave this with someone with in the school district. Probably by now it is on the access of VIA internet. If not you call apple explain to them this is a school thing they will lead you in the right direction. If this is a school with nothing but Apple computers Apple usually leave a source for contact to help in these kinda matters. Reason why I know I use to work for apple computers within the customer care center here in beaverton when they where here, and there is a protocol for schools to call and get any help they need with minimal and or no cost at all

^^ 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.

Yes there is firmware updates to this machine need to look closer

http://www.apple.com/downloads/macosx/apple/firmware_hardware/superdrivefirmwareupdate.html

just because it is out of the box means nothing. Why they are called firm wear updates.

FYI : just to let you know sometimes thing that say they are dose not really mean they are. Look at this link below think you might want to look into this if you fixing thing and doing admin stuff at your school.

http://www.apple.com/downloads/macosx/system_disk_utilities/secretfolder.html

Everyone is right, there is no issues with 7200rpm drives in eMacs. They are prone to unfathomable jumper issues however. Check the jumper settings on the old (OEM) drives and if possible one of the optical drives. If the old HDs are set to cable select, then it might be worth changing them to a master/slave configuration. I'm not sure which way around works best, you may have to try both. I know they are a pain to rebuild but sometimes its the only way, and once you have worked it out you won't have to work it out again.
Since they work in target mode for you to install onto, what Mac are you installing from? If you are using a Leopard image from an Intel Mac its not going to work. You need to do it from a PPC unit.

Firmware: http://en.wikipedia.org/wiki/Firmware

That update is for the Firmware on the Superdrive in those models. And also, there's a good chance his machine is pre-USB 2.0 because it's an ED model. But don't quote me on that. Unless there was a fundamental issue with the Superdrive that would prevent booting from another drive in the chain, I severely doubt that Firmware update applies.

When I said out of the box, I was referring to the fundamental Firmware update that applies to machines that ran OS 9.x before running OS X.
(http://support.apple.com/kb/HT1395)

The eMac does not have a machine Firmware update, only an update to the Superdrive which (most likely) doesn't apply to his model.
(http://forums.macworld.com/message/110839)

That's all I meant, not trying to be a jerk. 8)

Sorry trying not to come off like a jerk just simply giving you the facts to help to do your thing faster so you can do what you are doing faster correctly with what I know from personal experience. I own one of these for three years sold it a friend with 250 GIG HD and look every which way to make sure I was doing right. For dissembling a eMac is not the most favorite thing to do for those who own one or have had to work one. I am only working off what I see and really no major hardware info. I have now purchased a second one these machine and just upgraded it with a new 300 GIG HD and replaced the ram 1 GB and just installed a pioneer Super Drive. Then I replaced the back fan with a faster and quieter fan.

Firmware update are always good thing to just test to see if it will load into the machine if you do not know your hardware profile. Apple firmware updates for the hardware will either load or it will not because it dose look at hard profile info before installing. I am not trying to make you mad but trying to help you and give you what I find on my own time. If you look up earlier there is a person who quoted my comment and information trying show you that you need to make sure that this is set right, and meaning by check pinout means that every company has different place they have there cable select,slave,master settings in different places and sometimes rechecking this simple over looked thing can cause allot of headaches most the time it is what you are talking about. I hope that is not mean or hurt full. Just trying to help with makes a correct and fast installation that can be enjoyed. :-X

i tried upgrading the hard drive on my emac a long time ago,
it did not work because the jumpers were not in the right place,
but the information was on the manufacturers website,
so much fuss over a little piece of plastic

Have you tried formatting the drive in another Mac? In the past I have had to do that. Its worth a shot. I plan the same upgrade for the eMac I just got today.