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I have a nearly identical set-up (except I have the dual 2.5 Ghz G5).
Since I had similar experiences when adding/replacing internal hard drives in the past, I had the Apple Store replace the hard drive that came with the computer, with two 1Tb hard drives, and have had no problem.
The price of the hard drives was so low, that I figured it justified the extra expense in having them install it, plus this made them liable for ensuring that it worked optimally.
You may want to make an appointment with an Apple Expert at your local Apple store. Worst case, since you will only be out one hard drive, is to have the slow drive removed, dump it in an external enclosure, and use it just for storage/back-up, and have the Apple Store install you a new drive(s).
Good luck,
ADG
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