Effects plugins not working in Unity builds

Question

I teach an Audio Programming module at Abertay University. We're using Wwise (2019.1.7.7135) with Unity (2020.1.4f1), and we've run into a problem where certain effects plugins work fine in both the Wwise and Unity editors, but not in builds. We first encountered this with custom plugins (using the wp.py script to setup our project), but I've discovered the same thing happens with Wwise's own Pitch Shifter plugin.

The problem seems to reside in the build process: Before building, the Unity Import Settings for the plugin dlls are correct (e.g. the Standalone Windows x86_64 checkbox is checked), but after building, that checkbox is cleared. Investigating the build using Wwise's profiler shows a 'Plug-in not found' error. I can see that the Wwise integration hooks into the Unity build process, so I assume something is happening there to disable the plugins, but it's not clear to me why it would do that.

Any help would be much appreciated.