That it doesn't overwrite the backup is something that's not obvious (and if you've worked with other stuff that does auto-backups, it either automatically creates a backup(1) or overwrites backups instead of skipping over it) but I concede that's my fault.
However, when you run the installer and deselect everything but menu overhaul itself (no extra MO options or tweaks) not only did it backup everything (FF7.exe, battle.lgp, char.lgp, chocobo.lgp, coaster.lgp, condor.lgp, high-us.lgp, world_us.lgp, kernel.bin, kernel2.bin, window.bin, scene.bin and flevel.lgp) it also started unpacking the flevel with ulgp (which crashed at field 45, because that's the first custom field apparently and ulgp is still not something one can use with modded flevels) which then resulted in a pretty broken flevel. It returned the flevel all the way to the state of the backup flevel in my case which obviously was a disaster. I managed to salvage about 20% of the work by using the windows previous version function since I didn't expect the installers would mess with the files inside the flevel when I had no actual flevel function selected. (Unless MO wants to go and edit all the textboxes, which in itself would make it completely incompatible with any flevel changing mod like NT or N7 and definitely needs to be an extra option)
I pretty much accepted the loss and moved on. I still want to fix the .exe issue but then I'm probably gonna leave the mods for a while.
I'm using 2-1
Last modified 12/31/2012 (BootLoader.exe)
Steam re-release 2012
No, I mean the FF7.exe
The re-release could be an issue but I won't know until you give me the actual FF7.exe modified date