This is a weird one and I actually have a ticket escalated up to Microsoft but I was curious if anyone else has run into anything like this.
I'm trying to install an application called eClinicalWorks (or eCW for short). The installer for this application is not the best and I'm also working with the vendor on getting a working installer. However, they haven't had much luck with that either.
The installer has a problem that it doesn't register its OCX files with Windows correctly and it manifests twice after installing.
So when you first install it, I get a message from Intune that the install was sucessful but when you run as a regular issue you will get an error about a specific OCX file not being registered. I can fix this by having the install script (which runs as admin) launch the application after it's been installed and close it...