sorry i misread your post.
yeah your suppose to use sata ports 3-6 for your hdd.
i dont know how your bios options look like.
what choices do they give you in your bios where you hdd is listed? ide? ahci? raid?
i might be wrong but i think you need to might possibly need to provide a driver using the f6 method when installing windows.
your symptoms are similar to those who are installing ssd hdd's.
http://www.msi.com/service/download/driver-2743.html
here's a text file within the zip file that explains.
************************************************************
* 5. INSTALLING THE SOFTWARE
************************************************************
5.1 General Installation Notes
1. If you are installing the operating system on a system
configured for RAID or AHCI mode, you must pre-install
the Intel(R) Rapid Storage Technology driver using the
F6 installation method described in section 5.3.
2. The 'Intel(R) Chipset Software Installation Utility'
must be installed on the system after a supported
Microsoft Windows* operating system has been installed.
3. To install Intel(R) Rapid Storage Technology,
double-click on the self-extracting and self-installing
setup file and answer all prompts presented.
4. By default, all installed files (readme.txt, help, etc.)
are copied to the following path:
<bootdrive>\Program Files\Intel\Intel(R) Rapid Storage Technology
5.2 Windows Automated Installer* Installation from Hard
Drive or CD-ROM
Note: This method is applicable to systems configured for
RAID or AHCI mode.
1. Download the Intel(R) Rapid Storage Technology setup file
and double-click to self-extract and to begin the setup
process.
2. The Welcome window appears. Click 'Next' to continue.
3. The Uninstallation Warning window appears. Click 'Next'
to continue.
4. The Software License Agreement window appears. If you
agree to these terms, click 'Yes' to continue.
5. The Readme File Information window appears. Click 'Next'
to continue.
6. The Choose Destination Location window appears.
Click 'Next' to continue.
7. The Select Program Folder window appears. Click 'Next'
to continue installing the driver.
8. If the Windows Automated Installer* Wizard Complete window
is shown without a prompt to restart the system, click
'Finish' and proceed to step 9. If it is shown with a
prompt to restart the system, select 'Yes, I want to
restart my computer now.' (selected by default) and
click 'Finish'. Once the system has restarted,
proceed to step 9.
9. To verify that the driver was loaded correctly, refer
to section 6.
5.3 Pre-Installation Using the F6 Method.
Note: The Steps 1 and 2 can be skipped if you use the F6 Floppy
disk utility provided by Intel. These methods
are applicable to systems configured for RAID or
AHCI mode.
1. Extract all driver files from the installation package.
See section 7.2 for instructions on extracting the
files.
2. Create a floppy* containing the following files in the root
directory:
iaAhci.inf, iaAhci.cat,
iaStor.inf, iaStor.cat,
iaStor.sys, and
TxtSetup.oem.
* Note: For Windows Vista*, you can use a floppy, CD/DVD or USB.
3. For Microsoft Windows XP*:
- At the beginning of the operating system installation,
press F6 to install a third party SCSI or RAID driver.
- When prompted, select 'S' to Specify Additional Device.
- Continue to step 5.
4. For Microsoft Windows Vista*:
- During the operating system installation, after selecting the
location to install Vista, click Load Driver to
install a third party SCSI or RAID driver.
- Continue to step 5.
5. When prompted, insert the media (floppy, CD/DVD
or USB) you created in step 2 and press Enter.
6. At this point you should be presented with a selection
for one of the controllers listed in the Overview (Section 1)
of this document depending on your hardware version and
configuration.
7. Highlight the selection that is appropriate for the
hardware in your system and press Enter.
8. Press Enter again to continue. Leave the floppy disk in
the system until the next reboot as the software will
need to be copied from the floppy disk again when setup
is copying files.
************************************************************
* 6. VERIFYING INSTALLATION OF THE SOFTWARE
************************************************************
6.1 Verifying Have Disk, F6, or Unattended Installation:
depending on your system configuration, refer to the
appropriate sub-topic below:
6.1a Systems Configured for RAID Mode:
1. On the Start menu, select Control Panel.
2. Open the 'System' applet (you may first
have to select 'Switch to Classic View').
3. Select 'Hardware'.
4. Click 'Device Manager'.
5. Expand the 'Storage Controllers' entry (for Windows Vista* or later) or
'SCSI and RAID Controllers' entry (for Windows XP*).
6. Right-click on Intel(R) SATA RAID Controller.
7. Select 'Properties'.
8. Select the 'Driver' tab.
9. Click 'Driver Details'.
10. If the 'iaStor.sys' file is displayed, the installation
was successful.
6.1b Systems Configured for AHCI Mode:
1. On the Start menu, select Control Panel.
2. Open the 'System' applet (you may first
have to select 'Switch to Classic View').
3. Select'Hardware'.
4. Click 'Device Manager'.
5. Expand the 'IDE ATA/ATAPI controllers' entry.
6. Right-click on Intel(R) SATA AHCI Controller.
7. Select 'Properties'.
8. Select the 'Driver' tab.
9. Click 'Driver Details'.
10. If the 'iaStor.sys' file is displayed, the installation
was successful.
6.2 Verifying Microsoft Windows Automated Installer* or 'Package for
the Web' Installations:
1. Click Start.
2. Locate and select 'Intel(R) Rapid Storage Technology'.
3. The Intel Rapid Storage Technology application should
launch.
4. If the application does not launch, the Intel(R)
Rapid Storage Technology driver was not installed
properly and setup needs to be run.
