Internal Disk to Disk Data Transfer Speed Very Slow

I have a G5 Xserve running Tiger with all updates applied that has recently started experiencing very slow Drive to Drive Data transfer speeds.
When transferring data from one drive to another ( Internal to Internal, Internal to USB, Internal, Internal to FW, USB to USB or any other combination of the three ) we only are getting about 2GB / hr transfer speeds.
I initially thought the internal drive was going bad. I tested the drive and found some minor header issues etc... that were able to be repaired so I replace the internal boot drive
I tested and immediately got the same issue.
I also tried booting from a FW drive and I got the same issue.
If I connect to the server over the ethernet network, I get what I would expect to be typical data transfer rates of about 20GB+ / hr. Much higher than the internal rates and I am copying data from the same internal drives so I really don't think the drive is the issue.
I called AppleCare and discussed the issue with them. They said it sounded like a controller issue so I purchased a replacement MLB from them. After replacing the drive data transfer speeds jumped back to normal for about a day maybe two.
Now we are back to experiencing slow data transfer speeds internally ( 2GB / hr ) and normal transfer speeds ( 20GB+ / hr ) over the network.
Any ideas on what might be causing the problem would be appreciated

As suggested, do check for other I/O load on the spindles. And check for general system load.
I don't know of a good GUI in-built I/O monitor here (and particularly for Tiger Server), though there is iopending and DTrace and Apple-provided [performance scripts|http://support.apple.com/kb/HT1992] with Leopard and Leopard Server. top would show you busy processes.
Also look for memory errors and memory constraints and check for anything interesting in the contents of the system logs.
The next spot after the controllers (and it's usually my first "hardware" stop for these sorts of cases, and usually before swapping the motherboard) are the disks that are involved, and whatever widgets are in the PCI slots. Loose cables, bad cables, and spindle-swaps. Yes, disks can sometimes slow down like this, and that's not usually a Good Thing. I know you think this isn't the disks, but that's one of the remaining common hardware factors. And don't presume any SMART disk monitoring has predictive value; SMART can miss a number of these cases.
(Sometimes you have to use the classic "field service" technique of swapping parts and of shutting down software pieces until the problem goes away. Then work from there.)
And the other question is around how much time and effort should be spent on this Xserve G5 box; whether you're now in the market for a replacement G5 box or a newer Intel Xserve box as a more cost-effective solution.
(How current and how reliable is your disk archive?)

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### "myserver01" is a PV domU on Oracle VM 2.2.2 server running stock kernel ###
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87380 16384 16384 60.23 1.46
### Repeat the test in the opposite direction, to show TX is fine from "myserver01" ###
[root@myserver01 netperf]# ./netperf -l 60 -H myserver02 -t TCP_STREAM
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Attachments:
t3 - SCLK setup time.jpg ‏156 KB
Data byte Transfer_109.jpg ‏137 KB

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