Your firmware level is one of the factors attributing to the problem.
You should be at/about V2.8. Once you recover the drives
my recommendation is to upgrade your BIOS/Firmware levels/drivers on your system.
You will have to do the PERC bios in a couple of stages
before going to V2.8.
This level addresses these sort of issues you are experiencing.
See the Dell Support site :
(Important information about this package
===========================================
* This firmware package supports PERC 3/Di in following platforms:
-PowerEdge 4400, integrated PERC 3/Di, non-PAE only
* This firmware REQUIRES minimum System BIOS rev A11 PRIOR to flashing the firmware. Flashing this firmware to the system without first having updated to the above BIOS will render the system inoperable.
* Before updating your system to v2.8 level using Update Packages for Windows, please make sure your firmware level is at least v2.6 for your PERC 3/Di controller.
* PERC 3/Di on PE4400 servers using legacy firmware levels of 2.1.3 or 2.1.5 will require the following steps to assure a successful manual update to firmware revisions 2.8.x.
Steps for manual update from firmware v2.1.X to firmware v2.8.x:
To assure a proper update to the PERC 3/Di Windows driver version 2.5 or later, it is necessary to apply the driver 2.1-5 patch prior to updating to the driver version 2.5. Failure to install the
driver patch may result in a system hang followed by a blue screen error during the reboot.
***NOTE: This patch file is not included nor is it needed with PERC 3/Di driver versions 2.6, 2.7, or 2.8.
The driver upgrade patch is only required on systems using older PERC 3/Di 2.1.x firmware/driver code running Windows 2000. Systems already using version 2.5 can be updated directly to version 2.7.0 or higher without problems.
To update to version 2.5:
Run the 2.1.x driver patch (p3patch.bat) included with the Windows 2000 2.5 driver download files.
Update the Windows 2000 driver to 2.5.
Update the firmware to version 2.5 when rebooting the system.
To update from version 2.5 to version 2.8.x:
Update System BIOS PRIOR to flashing the firmware. Minimum system BIOS required is A11.
Update the Windows 2000 driver to 2.8.x.
Update the firmware to version 2.8.x when rebooting the system.)