Ok I figured out what happened and I'm an idiot!
Hopefully others may learn from this.. a major DOH!!
When I moved some of the mods into the MODS directory, I didn't pay attention to the subdirectory structure and was moving a folder that was "two layers deep". For example let's say I downloaded a MOD called "New Something".. well.. after unzipping I had the following: "C:\New Something\New Something"
. So for my problem, I had downloaded a patch for the FM interior that was supposed to be installed after MaGUI.
The folder was \MODS\FM_NI_Fix_for_MaGui F\FM_NI_Fix_for_MaGui F\..
So I just made sure that there was only one level of directory.
I hope this makes sense
Now everything works!