UnrealPak ignoring directories in 5.1

I’m creating pak files with UnrealPak.exe and simply put, the 5.1 version puts every file in the same directory.

This is using the 5.1 exe

And this is using the 5.0 exe

Is there a setting somewhere that changes this behavior?

Edit: Fixed it by writing out the command directly instead of using a txt file, no idea why the 5.1 exe behaves differently but whatever