I had exactly the same issue, but now after 2 days frustration I found the solution, also thanks to your post.
When I inserted a 3T WD Caviar Green, it got recognized as 746 GB disk in the user interface. In fact, WHS creates a 746 GB partition.
Installing the latest version of Intel Rapid Storage Technology solves this problem, but it does not remove the partition that was created for you. So it stays a 746 GB disk. Any new disk you insert gets recognized as a 3 TB disk (but actually it is wrong, see below).
To solve this, I needed to use a Remote Desktop connection and go in to the WHS server. Right click My Computer, select Manage. Open Storage, than Disk Management.
Here you can see the small partition.
Remove the disk from the WHS UI using Server Storage to make sure there is no longer any data on it, and the following actions do not interfere with the WHS administration.
Now in Disk Manager, remove the partitions, and create 1 new 3T partitition, quick format it and give it a suitable name.
If you have -like me- a Western Digital Caviar disk, you can download a utility from the WD site to align the disk, I understand this is needed under XP and Windows Server 2003 to increase the performance. Alternatively, you can hook up the disk under Windows 7 and format it there, this will make it aligned automatically.
Now you may need to reboot, but then you can add the disk as 3 TB disk for back up purposes.
Using a 3T disk for internal storage
If you want to use the disk as internal storage, the situation is more complicated. As soon as you add it, it is changed from a GPT disk (which can hold more than 2.1 TB of storage) to an MBR disk, which can only hold 2.1TB. In my case the WHS user interface counted it as a 3T disk after adding, but if you look in the Disk Management, you see it is now 2047,99 GB with an unallocated partition of 746,51 GB. This will happen to any 3TB disk you insert.
If you really, really want to use the 3T for internal storage, you have to follow the instructions
here, with the following remarks.
a) WARNING, if the UI of WHS shows a 764 GB disk, do not start. Make sure you update the drivers first (Intel Rapid Storage Technology), so it gets properly recognized
b) WARNING, you may mess up your backup database if you do it incorrectly. If you are not used to registry editing, don't do this.
c) Change step 10 and 11 in the guide on wegotserved to this:
10) Recreate the partition as a GPT partition if your goal is to use a greater than 2.1TB volume. Once you are done creating your partition how you would like, Give it the label "DATA" and mount it back in the old mount point (c:\fs\*) (for example I mounted mine back in as C:\fs\1K) It is critical that you label it correctly and mount it correctly here in this step.
11) Copy your files back into the mount point that you copied out in step 7, copy them in as they were before you deleted the original partition.
Now use the align tool to align the new disk. Select the correct (empty) disk and realign it. In my case it required me to reboot. Reboot first before you continue. After reboot, do step 7 in the guide again to stop the services.
After this, go back in the Disk Management tool. The realignment process added a drive letter to the disk, in addition to the c:\fs mounting point. Delete the drive letter (Right click, Change Drive Letter and Paths), leave the mounting point.
Now continue with step 12 in the guide. Note that after step 12 there is a new step 11 and 12, so make sure you start with the first step 12 and follow the instructions in sequence.
I'll hold off getting one for now then 
