Josh,
The ntoskernel.exe is the running "kernel" of the server, so if you replaced it with a "backup kernel" or one from tape it will not work cause the old kernel is the one with additional modifications to it.
Every time you change add or subtract stuff from you server it mod's the ntoskernel.exe.
Rebuild the server and dont resstore the ntoskernel.exe, just restore the DR stuff. If you have a copy of the new ntoskernel.exe move the other one to the junk pile and replace it with the new one.
Cool....
JD