Well, after a not-so-fun week, I was able to resolve the issue and get the drive back to 3TB. I want to thank you guys for your help. If it wasn’t for you, I’d probably be waiting for a replacement drive right now. Regarding the BIOS updates, let’s just say that Gigabyte’s English isn’t the greatest so the descriptions of the updates are probably not entirely accurate
For those who might be in a similar situation, here’s how I fixed the issue:
fzabkar was quite right that my drive had been truncated. It probably was the BIOS of my Gigabyte board (P35-DS3L), even though I’m 99% sure that this particular drive had never been at the top of the boot order. Regardless, I’ve tried all kinds of things. I wanted to try HDD Capacity Restore, but it doesn’t run on 64 bit operating systems and I didn’t have a 32-bit system handy, so that was out. I also tried to use HDAT2, but I couldn’t get the boot CD to work so that was out. After some Googling I learned about Parted Magic. Well that’s Linux and I’m a Windows man so that was a little beyond me and I abandoned it. It very well could’ve done the trick as well, but it wasn’t my cup of tea so I decided not to press my luck. After that, I read about MHDD. Through reading about MHDD I discovered Ultimate Boot CD, which happened to include this utility. So I downloaded that and ran MHDD but it always said my drives weren’t ready. Gave up on that and noticed that HDAT2 was also included so I tried that. Well that disabled my keyboard (which could’ve been an error on my part), so THAT was out. In browsing the list of diagnostic utilities I spied SeaTools (2 versions, 1 with a GUI). I remembered that so I ran it. It was extremely easy to use. I selected the drive and it showed me how it was indeed truncated, so then I went into one of the menus and selected reset to max factory capacity. 10 seconds later it was done. I rebooted into Windows, loaded Disk Management, and there was my drive, all shiny and new with 3TB. I converted it to GPT and I’ve partitioned and formatted it and all is well. To prevent this from happening again (I hope), I’ve also updated my BIOS to address this particular bug.
Hopefully my journey will help others. If you’re running a 64-bit OS and don’t have access to XP or another 32-bit OS for HDD Capacity Restore, give Ultimate Boot CD a try. As a semi-last resort I was going to format my Shuttle PC and put XP on it to fix the drive. Thankfully I didn’t get quite that desparate. 
