Deploy System state error

[koolaidkitten]

My fileserver's O.S drive decided to take a crap on me so I had to reinstall Server2k3 Standard again. However I did have a month old ntbackup of the systemstate. This is my first time I ever tried restoring using that. What I did was format and install Server2k3 to a new drive, install all drivers and all windows updates.
After that I deployed the systemstate. Then after making sure ActiveD, DHCP and DNS was working and it was talking to the PDC *this box is also an additional domain controller* All of that seemed fine. So at this point I decide to install all my apps and utilities. This is where the problem comes in. I guess the system state also records data about your installed apps, this new setup THINKS that it has all my previous apps installed, however they are not really there. if you go to "Add remove programs" I can see all my old apps, however upon trying to remove or reinstall them the process is halted with an error basicly saying I can't find this or that. This also goes for windows updates as I think it is trying to install updates that the server previously didn't have, but now that I reinstalled and updated to the absolute latest, then rolled out that ntbackup systemstate, it thinks it does not have them.
Anyone know how to fix this issue?