After runnin Windows, BIOS wont detect drives

[n00by]

Hi, I have a strange problem with two of my hard drives.
I have 3 spinpoint F3 500GB in my WHS 2011. the motherboard is a Gigabyte 525TUD.

two of my HD's i use for storage, and it is these HD's i have problems with.

when i started using my server i first had ubuntu server as OS, and i tried both SW RAID and RAID on my motherboard
on the HD'd ment for storage use. After i while i convert to Windows Home Server 2011,and also there
i struggle some times with RAID setup, before i formated the disks and used them in normal setup.( I use the backup function in windows to backup one disk to the another one).

The problems i have now is that BIOS wont recognise the two HD's, IF I'm NOT RUN LINUX ON CD/DVD FIRST!

If i run linux and then restart, BIOS detect the HD's without problem. if I'am NOT run linux, BIOS wont detect the HD's, but use more time before it boot windows from the third HD.

I have format and erase MBR on the HD's, without success.
Anyone knowing what the problem could be???

 

[n00by]

It is an AOpen ao350-12ahnf.
The PSU is the only part in the Server who is used before.
FYI i have also tried to connect the HD's, who I have problems with, to an second PC with an SATA to USB adapter. I get problem also there and only find it as an non-initialized USB device. when i try to initialize from disk management(windows), i can't.

 

[n00by]

i'm not an HW expert, but anyhow i think my problem is not typical an newbee-mistake with an obvius solution... 🙁
What is making me confused is that for me it look like some information is loaded to BIOS or into HD when i start Linux from DVD, and also the same information survive an restart and makes the BIOS detect the HD's. Could that be possible?