Some clarification regarding the comments above...
The MD3000 is a box you SAS-cable directly to a host and can be used by that box only. The MD3000i is an iSCSI target that you connect to the network and then use an iSCSI Initiator to connect to disks. The boxes look identical on the front but obviously have different connection mechanisms. The firmware for them is not the same so you do need to be sure you have the right stuff.
I'm not sure about the link previously posted but do this: go to dell.com, click on support, click on Drivers and Downloads and then select the PowerVault MD3000. You'll be able to pick your OS so pick 2003 x64. You'll then be presented with a long list of potential downloads. Download the MD3000 Resource CD - it is an ISO image. This CD will include all the latest documentation and firmware for the MD3000.
With this, you'll want to do 3 upgrades:
1. NVSRAM (I know you said you did it already but do it again just in case so you have the most recent version)
2. Controller firmware (this is the upgrade that actually enables partitions larger than 2TB; most recent versions also add RAID6 support)
3. Disk firmware (you may have to run this multiple times depending on how many kinds of disks you have)
Don't race into the 3 steps above - read all the documentation about each step to make sure you're doing it right.
You mostly need the controller firmware to get what you want but you do want to be sure that you are running compatible and upgraded versions of everything at the same time so you don't have issues down the road.