I also encounter similar issues with Eziriz Rector and Intellilock recently when I received Windows update including 3rd party software updates.
I have to "protect" my application by de-selecting all protection options, then adding each option back one after another to find out which is causing problems with other software. For example, just last month one option causes the application to be recognized as a "mal-ware" by Avira after the antivirus software get updated.
I think the bigger problem is we have no idea what 3rd party software the clients have on their machine, and yet I have to programmatically find out the compatibility issue before installation of the distribution. Perhaps someone has better ideas.