Cannot format drives or assign drive letters after changing SATA RAID controller

I'm running a Windows SBS 2003 box with an Intel SE7210TP1-E motherboard, an 80Gb IDE drive for the system, and a 160Gb  RAID 1 SATA array attached to the onboard Adaptec Hostraid controller that is set up as an extended partition containing two logical drives (D and E) of 120Gb and 40Gb for data and mail. This setup works OK, but I acquired an Adaptec 2410SA hardware SATA RAID controller I wanted to use instead of the software Hostraid.

I backed everything up on the existing RAID 1 array, unmounted the Exchange stores, then shut down the server completely and removed the two WD 160Gb drives. I powered up the server as far as the BIOS setup, disabled the Hostraid controller and switched it off again. Next I installed the 2410SA with two new 160Gb Seagates and configured them as a RAID 1 array using the ARC BIOS utility, then finally booted into SBS 2003 and installed the drivers. Apart from expected complaints from Exchange, the real trouble began when I tried to configure the array with Disk Manager. Basically, nothing worked!

I could initialise the volume using the Initialise and Convert wizard, but I couldn't format the drive or assign it any drive letter. If I chose to not assign a drive letter or path, that didn't work either, merely generating terse and unhelpful messages about internal errors and the format not being able to complete. If I quit Disk Management and opened it again, the Initialise and Convert wizard would appear again and invite me to repeat the whole procedure. If I plugged in a USB flash drive, that was assigned drive letter G:, and not D: or E: as might have been expected. It appears as though Windows 2003 remembers that there was a D: and E: drive and prevents their assignment to removable drives, but why won't it allow any drive letters to be given to the new disk array, and why can I not format it?
Adaptec's Storage Manager reports nothing amiss.

Both the Hostraid and the 2410SA have the latest firmware and drivers, and I have installed the latest version of Adaptec's Storage Manager.

Is there a realistic prospect of simply moving the array to the new controller and expecting it to work, as both are Adaptec?  

I've trawled EE and the web extensively, but to no avail. I am probably overlooking something obvious, but maybe I've been too close to the problem for too many hours now...
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DisorganiseConnect With a Mentor Commented:
First off, disable all exchange services so they aren't trying to access the disappeared drive letters.  Repeat for any other services you have like SQL, IIS etc that use your D and E drives.  That should allow for reboot without error messages if its done right.

The inability of the OS to see the drive properly suggest a dodgy cable - I realise the controller see the drives fine, but let me share a recent experience:  we have a recently installed SAN and had a SQL box configured with dual paths to the SAN.  3 of the 4 LUNs worked fine, the 4th would not format.  After some troubleshooting, it appeared the dual pathing software was installed badly and so we re-installed but still had odd issues like the entire server locking up solid.  A full OS re-installed had no effect.  we eventually worked out the cable connecting the racks (not the server to the patch panel) was dodgy and used another port - voilla, all good.  Through all this, the switches etc reported an occassional CRC error but that was it.

you may also need to remove the old drivers as they may be confusin each other.  Also try safe mode to see if the drive letter appear - you may have to tell the OS they're gone
PerarduaadastraAuthor Commented:
That's OK by me.
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