So, I have been having trouble with some of the dev tools (futuratop.bat) and 3rd party tools (mikeros pboproject). Turns out it is because the value in the registry key at "HKLM\SOFTWARE\Wow6432Node\Bohemia Interactive Studio\ArmA 3\main" is set to the wrong value. In my case it should be "D:\SteamLibrary\steamapps\common\Arma 3" but was "D:\Steam Games\Arma 3". I corrected this manually and fixed my issues.