Mod Organizer crashes on launch, but works when 'run exe on prefix'

I have set up a prefix to run Mod Organizer with Stalker GAMMA.
Everything is set up right - I can play the game. However, this is posted because I think I have found a bug in Heroic.

Launching Mod Organizer via 'Launch' causes Mod Organizer to crash with files not found, I suspect due to its virtual file system being unable to be started correctly

However, if I use the same prefix and same executable but run it via the 'run exe on prefix' button - it starts correctly and everything works.

Why? Why are the two methods doing it differently and how can I make it launch without having to do the tedious exe on prefix method?

log - https://pastebin.com/T00RjwU5 (both methods output the exact same log, so I have only included one log here)
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