Ok first a little info about my server.

q6600
ga-ep45-ud3p
8x1TB samsung disks
6x ich10r sata
2x jmicron  sata 20363 AHCI
1x jmicron IDE 20363 AHCI
120gb samsung spinpoint PATA drive connected to jmicron along with a dvdrom
PCI0680 Ultra ATA-133 Host Controller as the alternative IDE controller then 
the jmicron

A little background of what i want/have setup:
I have setup a 6000mb raidz2 storage array, and i run VM's for windows and 
Ubuntu to serve anything that i cant do so on OS, like daap firefly server, 
utorrent, encoding etc. This has been fun and a good learning experience 
setting it all up and everything is working perfectly accept for a few things 
which i will explain now.

First problem i had was a single drive kept having write fails and the raid was 
becoming degraded, so i tested the drive and it passed all tests and then moved 
onto checking the ports/cables and found out that it would fail every drive 
that's on that one specific port. The motherboard i was using was a p35-ds3r 
which already had broken sound so i figured the board must have a faulty port 
and i brought a new ga-ep45-ud3p after reading that it works really well with 
OS. Now i put it all back together and i get the exact same error's and had a 
fit as i just spent a lot of money on a new board for nothing. I remembered at 
this point that DVD ROM's and jmicron dont tend to get along so well, and after 
pulling it out i stopped having the failing drive. This was good news as i did 
not need a DVD ROM after installation, then while transferring files from the 
system drive to the raid i was experiencing a new problem, the whole PC would 
stop responding. So that's when i fished around a
 nd found an old Silicon Image 0680 IDE controller and threw that in. Now 
everything seems to be working with no errors and no crashes BUT. Now 
everything to do with the system drive goes so slow, and im talking about 
taking 2 hours to copy a 4gb file, to load a VM about 10-20 minutes etc.

At the moment once the system loads its working... slowly, and this is good but 
not a long term solution by a long shot. So i tried out booting the system disk 
from USB, this was a promising idea as it leaves more space in the case for 
more disks in a later expansion. But as usual this presented another problem, a 
disk with an NTFS partition can boot fine, but any disk with OS installed on it 
causes the PC to hang at post... im guessing this is when its scanning the 
disks in the system.

This is my horror story so far and if anyone has any idea's of whats going on 
could they please help me out, anything that gets me full speed system disk 
without costing a bucket load more of money would be great. My next option im 
thinking about is buying a 
http://www.sunix.com.tw/it/de/Product_Detail.php?cate=2&class_a_id=34&sid=367 
but that's going to cost me $80 and then on top of that i need to buy a new 
sata drive as i do not have any more. plus i believe silicon image controllers 
aren't that well supported.

Thanks for reading and any help you may give
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