2006 Mac Pro corrupting the disk - possible logic board problem?

Hi there.
I bought a faulty MP (2006) that wouldn't install an OSX. It would install to a point and then fail or install fully then not boot. Apparently this happened shortly after a 10.5.8 update failed mid way. The seller told me how it seemed to corrupt hard disks placed into it. How he diagnosed this I don't know.
I bought it and did a fresh 10.6 install on a formatted disk in my other 2006 mac pro. Then swapped the disk into the faulty mac pro. Everything seemed fine. Booted up and seemed to work fine.
Upon trying to install itunes 9 I had all sorts of issues (which I've read about). Upon doing a disk check in disk utility it seems the disk has loads of errors, imcomplete nodes/trees etc. Repairing the disk isn't working (in the OS as well as booting from the DVD).
Has anyone encountered anything like this? It seems the disk is getting corrupted by something or other. Hardware tests check out fine.
Could this be a problem on the Logic board?
Thanks

One thing I did notice that I thought was odd was on the grey boot screen a small empty progress bar appears for a second or two and then vanishes. Sure this is the same progress bar that appears on an efi update etc.... not sure it's connected

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    EAX: 0x7db19000, EBX: 0x07eb6004, ECX: 0x0ff00000, EDX: 0x0ff00000
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    0x4469ba98 : 0x2203de (0x6b08cc 0x4469bab8 0x229fb0 0x0)
    0x4469bac8 : 0x2ceabf (0x6bd9e0 0xbaf978 0xe 0x6bd989)
    0x4469bb78 : 0x2e5564 (0x4469bba0 0x4469bb88 0x4469bb98 0x22cbbb)
    0x4469bb98 : 0xbaf978 (0xe 0x44690048 0xff1b0010 0x10)
    0x4469bc38 : 0x1547167 (0x8ad2c04 0x7eb6004 0xff00000 0x7eb6004)
    0x4469bc58 : 0x153e35c (0x7eb6004 0x8feab04 0x0 0xff00000)
    0x4469bc88 : 0xcb6c56 (0x7eb6004 0x9465004 0x4469bca0 0x0)
    0x4469bd38 : 0xd27c8a (0x7eb6004 0x9465004 0x8971c14 0xff)
    0x4469bdc8 : 0xd2933e (0x7eb6004 0x8a97c04 0x0 0x0)
    0x4469be28 : 0xd2b46a (0x7eb6004 0x8a97c04 0x8 0x2)
    0x4469be58 : 0x1562269 (0x7eb6004 0x8a97c04 0x0 0x0)
    0x4469be88 : 0xd2b589 (0x7eb6004 0x8a97c04 0x0 0x0)
    0x4469bed8 : 0xb9eb05 (0x7eb6004 0x0 0x0 0x0)
    0x4469bf68 : 0xb5362c (0x7eb6004 0x1 0x7c637f0 0x7c63be8)
    0x4469bf98 : 0x23e4ae (0x8af4400 0x7eb6004 0xfa6d03 0x7eb4028)
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