Nope, that didn't fix it
While using official releases of ID and IC updates fixes the Extensions Manager issues, it still leaves open the question why InCopy CS6 is having this missing Plug-Ins issue. I looked back at InCopy CS5 and opened an article from the previous issue and examined associated plug-ins and no problem. I examined the plug-ins associated with articles attached to layouts in InCopy CS5 and the Package and Preflight plug-in is listed, but InCopy CS5 is handling it fine.
I compared InCopy CS5 and CS6 plug-ins. CS5 has the Prepress Plug-ins folder, CS6 doesn't. For some reason our InCopy CS6 Installer isn't installing these plug-ins.