Alright, so I finally solved the issue. The Run key was not being
executed because I had manually set the Shell registry key in TD. So
whatever processes the Run key was not being set to do so because I
still had the Explorer Shell component in my build. It was only after
I removed the Explorer Shell and added the Command Shell, that the Run
key actually executed at every boot.

Thank you Mike, it was the link that you suggested that gave me the
idea. I checked the UserInit key in the registry and it was not set to
"C:\windows\fba\fba.exe -run" when I manually set the shell. However,
after disabling the explorer shell and adding the command shell, that
value data shows up in the Userinit key.

After a little more testing I believe that the Userinit registry key
is not the only one required to make the FBA process the Run key. I
built an image using the explorer shell and then manually set the
shell to "cmd.exe" and Userinit to "C:\windows\fba\fba.exe -run".
After doing this the run key was not executed which would inidicate
there are other things that I did not set manually. So this is not
something that I can set manually unless I know all the registry keys
that need to be set. No matter, I will just have to configure my image
a little differently from now on.

Thanks again all.

Kyle