Mac Pro 2.1 Strange HD issue

Been Having HD issue with an early MacPro(2.1) Dual Quad core
Have changed the boot disc 3 times, have reformatted the discs and reinstalled from CD on numerous occasions, then allowing time machine to restore my normal environment.
Eventually i took the The Mac pro into an Apple approved repair centre they had it for two days and claimed to have run every diagnostic test they can and can find no issues with the Mac pro of the discs.
They have suggested a clean install of everything no use of the time machine backup.
Then they said that the manual stipulates that this Mac Pro can only handle 2TB of HD space in 4, 500 meg discs they said as i have 4, 1 terabyte discs in the macpro and this is the only thing they think is causing the problem.
Anyone have any thoughts on this
Symptoms a couple of weeks after new disc or the reformatting of a disc
The Mac Pro would start to slow down and i would have lots of beach ball spinning issues some apps especially mail would be come very unresponsive.
Running Disc utilities would always report a damaged boot disc But never reported any issues with the other Terabyte discs and to be fair I was having the same issue with a 500Gb disc that why i changed the boot drive and upgraded. things came to a head when i ended up with a grey start screen a progress bar followed by a shut down even when trying to boot from a the install CD
Any thoughts much appreciated

Graeme,
You are posting on an iMac forum. I'd recommend posting to the correct MBP forum. I will ask the moderator if he can move your post for you.

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