Missing partition in 2003 Enterprise Edition

What happened recently after a breif session of using it is that I
encountered a blue screen of death and my system wouldn't start up again
properly.

So I managed to get it at least up and running again with the recovery
console, unfortunately, the partition for all my files seems to be gone. At
least according to the system anyway.

Now I can see both partitions and they are fine according to diskpart and
the numerous other software I grabbed to try and fix this problem. Fixmbr or
Fixboot doesn't have any effect either.

Why is it that every other program, can see that drive, even in the recovery
console, I can navigate it as well, but the OS itself thinks it's running on
a 5GB HDD and all the links to the software I have installed are missing
because of this? How would I fix this?

Open up Computer Management from Administrative Tools and go to Disk Management.  Make sure all your partitions are activated and healthy.