Scoton:
For some people, it takes a bit more effort to REALLY disable PepperFlash... Chrome automatically re-enables it without notice! See my profile blog for details.
Just looked at your blog post. It's very well written. It should made into a sticky.
When I had the problem I didn't have two flies, only had "pepper". With my dumb luck I made the second one and disabled "pepper". I now keep the plug in page as a bookmark/favorite and check it from time to time to make sure "pepper" is disabled. What can be confusing is the wording to enable/disable. When it say's enable on the bottom, "pepper" is turned off (disabled) and that text area is grayed out.