i fell asleep there....
it's clear that the process of opening the plugin at start-up is creating a different output than the process of adding a plugin in real-time. i'm back to the initial question: which one is corrupt?
this is harder to figure out because i don't have a baseline.
i'll have to test to see what happens upon opening, removing and replacing. if that nulls with the original files then it is definitely a difference at start-up. if it doesn't, it suggests something in the project file.
i'm also going to post to some forums, as i now have a specific question.