Could there be something wrong in your manifest file or some other settings file? Some relative path pointing to a folder in your source hierarchy? Maybe it is just an image file or some sort of settings file that is missing? Or it might be something completely different.
A I wrote in your other question, one approach for hard-to-debug dependency scenarios is to just bite the bullet and run a thorough procmon.exe session (that is a direct hotlink to the live sysinternals tool share, clicking it will start the download instantly - just so you are aware).
You can see a quick description of how to use this tool in this question: Registering a CPP dll into COM after installation using Wix Msi installer. The key is to set an include filter which will show only events you need to see - basically for your own application.exe should suffice I believe.
Many find this procmon-stuff overkill, and don't want to deal with it - but trust me, it almost always reveals something unexpected (not always useful however).
As before this answer may also be worth a quick skim (on dependencies in general): After creating MSI Installer for WPF app in Visual Studio 2017, EXE does nothing. I would at least try the Dependencies.exe tool - even if it is a bit "beta-ish". You can download from here: https://github.com/lucasg/Dependencies/releases.
And certainly double-check the modules view in Visual Studio which I describe in the linked answer (Debug => Start Debugging
, then go Debug => Windows => Modules
). It should show whatever was loaded to run your project interactively.