I can't reproduce your problem. Even if I set Tools>Folder Options to "Do not show hidden and system files" in stead of my usual "Show all files" they turn up in the right pane: Shockwave Flash, Java Runtime, WMP codecs. So my question is: how to set WE to NOT see the contents of downloaded program files.
Try a simple viewer as Gyula's navigator from http://www.tucows.com/preview/195761 (free). It gives a more 'real' view of the disks content than W.E.
Active X cache.
If I use W.E. and go to windows/downloaded prog files and then select properties it says
Is there a way with W.E. to see these files and folders?