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Nope, They should all run fine. But if you want to, go in sequential order, SATA ports should be listed on the MB from 1 to whatever many ports there are, so I guess set your system HD to the first one and the rest, use them in whichever order. That's what I do on my computer at least.
No, it doesn't make a difference. That's an odd problem though. I have my drives set to AHCI mode and my motherboard has no trouble detecting everything.If I want to set my drives to ACHI, does it matter which ports I put my hard drive and DVD-ROM?
When I try to set ACHI mode in my BIOS, the motherboard no longer sees my DVD-ROM so I can not install Vista. Once I set it to Raid or IDE, my DVD-ROM appears. If I want to set my drives to ACHI, does it matter which ports I put my hard drive and DVD-ROM?
There are some lame raid ports you can't use optical drives or even regular drives on.
For example the lame ass Asus xpert raid on the P5Q boards. Its slower than the ICH10R raid and you can't use it for non-raid or optical. Kinda like you got two cripple sata ports. It takes a bit of jumping through loops and holes to get it working for non-raid hard-drives though.