Product and version FileMaker Pro Advanced 16.0.0
OS and version Mac OS 10.12.5
Hardware Recent iMac
Preferences > Plug-Ins doesn't update when a plugin is updated ( not installed ) via the Install Plugin script step.
How to replicate
Install a version of the BaseElements plugin, such as 3.2 manually ( quit the app, and then copy to the correct folder etc ). Check that the preferences and Get ( InstalledFMPlugins ) function returns the correct plugin versions. Run the Install Plugin script step with a newer version of the plugin ( such as 3.3.4 or 4.0b2 ) and check that it installed via any error code and that the Get ( InstalledFMPlugins ) shows the new version.
Open the prefs, and it still shows the previous version.
None that I'm aware of. I'm also not aware if the code in the plugin has to do anything to force an update on load, as far as I'm aware this is outside of the plugin API and something that FileMaker itself manages.