New HD won't run without old one...

hello.
After lots of help from my educated peers on this discussion site, i installed a 2nd hard drive into my G5 quad power pc.
I then used carbon copy cloner to clone the old drive onto the new one(because i recently moved and forgot my install disk on the west coast), and when i re-booted, i was able to boot from the old HD (which still barely works), and then i was able to select the new HD in system prefs - startup disk, and then re-booted agian, and it would boot up on the new HD, and work great.
And every time after that, it would always boot from the new HD, and work fine.
Except that the old HD is still in the other bay, apparently working in conjunction with the new one.
I know this because I cannot get the new HD to boot if it's the only HD in the machine. I tried both HD bays.
I even tried to boot up while holding down the Option key, but the HD won't show up at all. Tried both HD bays.
Any thoughts?
I'm having my friend ship my my install disk, but if carbon copy cloner is as good as it says, i shouldn't have to do a clean install and have to go through the hassle of doing a full backup, and restoring....etc..etc..etc.
Any thoughts?
i tried every combination of HD bays with both HDs.
The new one just won't work by itself.
And, the old HD needs to be in the top(primary bay), or else nothing works.
thanks!

Ya know, today, my Mail program is acting very funky.
I launch it, and I get the spinning color wheel immediately, and then it quits itself.
Also, when I reboot, i see a quick flash of weird graphics on the monitor for a split second.
Doesn't look right.
Oh, and now, I'm finding out that the machine randomly reboots from either HD.
I just tried to reboot, and it tried to boot from the old HD in the other bay. ( i know this because the old HD takes 5 minutes to boot, and the internal fans run at full speed during the whole boot up process ).
Now, i tried to reboot again, and it booted fine from the new HD>
Weird.
maybe i'll try super duper.
Problem is that the old drive took 2 full days to clone when i used CCC.
The old HD is so sluggish that it is barely usable.
Hopefully i can get a full clone out of it.
Regardless, i'm just going to have to do a clean install to feel comfortable about this machine at this point.

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