I managed to track this down and fix it. The cause was as follows: if duplicate morphs were found, the 1st one in alphabetical order would be chosen as the one that was the parameter that could be controlled by triggers. Depending on the name of the package, it could come after the local Custom morph. In that case the scene would set the morph from the package, but the trigger would control the local Custom one instead. This often led to morphs getting double set in the scene.
I have fixed it so already active morphs are considered 1st when registering the parameters. That way whatever morph the scene might have set will get priority as the one to use for the parameter.
Fix will be in 1.20.1.5 release