Perhaps this is the problem
I keep wondering why InCopy CS6 will complain about a missing plugin if it is attached to a layout created from an template as opposed to a layout created from scratch. In both cases, if I examine the article, there is a missing plug-in reported, but only in the former case is there an obnoxious dialog box. I am suspecting that trigger is our use of a custom preflight profile that we put in our InDesign templates. I will work on this theory today.