For Flash, I'd try uninstalling it and reinstall. Try using the uninstaller from Adobe:
http://kb2.adobe.com/cps/141/tn_14157.html
I've used it in the past when I had issues w/ the installation. It will remove all Flash from the computer, including the ones for IE, if I remember correctly.
For Java, I think you've said that you've uninstall and reinstall it. Have you cleaned up the registry in between install? Not something I typically do unless I encounter problem. Like in your case where some files didn't appear to be installed properly.
Can't comment on installing older version of anything. Haven't had any issues where upgrading broke something.