You have archive scanning enabled then...
I'm not sure why you'd want to enable that setting. It has been investigated at length that disabling archive scanning is of little/no consequence. Even so, for those environments that must have it enabled, there are ways to reduce the time needed to scan archives - rather, ways to avoid scanning them.
The simplest of which is to submit your file to McAfee Labs to have it whitelisted in our DATs. As long as your file doesn't change, it won't endure a lengthy scan. Another (which we won't see until patch 4 in September), is making use of our Artemis/GTI technology, to get a quicker response from "the cloud" as to whether the file is "known good" or not - this exists in Patch 3 today but that patch only benefits Win8/Srv2012.
When we release new Engine versions, that too may provide overall improvement to scan times but it's not a guarantee.
You are right - we do scan archives, so that viruses could be detected before extracting/executing or for scheduled jobs, to detect viruses in older files/archives.
So, if I understand it right, jqs.exe might not be the problem, but rt.jar, because it is handled like an archive?
I'll try disabling it to see the difference