I'd suggest trying to move the BAIN folders to more discreet locations. Even further separation where they don't share the same file path with only one small difference.
Here is the file paths that I have for my bash ini files:
sOblivionMods=I:\Games\BAIN Archives\Oblivion Main Mods
sOblivionMods=I:\Games\BAIN Archives\Oblivion Alt 1 Mods
sOblivionMods=I:\Games\BAIN Archives\Nehrim Mods
- I'm thinking either mTES4Manager or you are being confused at what is pointed where. Like perhaps there is one extra layer of folders called Oblivion Mods.
Also if using Wrye Bash 291+ the ini changed for Bash.ini and if you made your custom paths with an older bash then I'd try adding those lines to a new bash.ini
And I did none of this directory adding/moving through mTES4Manager - I did it all by hand. I only use mTES4Manager for switching installs and that is it.
Make sure each install has its own bash.ini??