The proper VST scanner version for Kingston is 5.4.1.0. Its still somewhat mysterious how John got the older version on his system. We had a prior release candidate installer that had 5.4.0 but we didn't ship that version.
My best theory is that somehow John's machine got delivered a previous binary from Amazon and its stuck in a cache somewhere. Which country are you based in - it might be relevant from amazon's caching point of view? Its pretty hard to diagnose stuff like this over email so I think a support person will have to do more testing with him when work resumes on Monday.
The only problem with 5.4.0 was the first scan problem he ran into. After that it fixes it self up so its not a huge issue despite being disconcerting to see. The scan itself won't affect the operation of plugins.