Hmmm, he mentioned "leftovers" from previous installs of java. Many packages can be reinstalled over the top of an existing install, but not in the case of java: its best to make sure any present install is completely uninstalled before upgrading. These "leftovers" *may* be what are causing the mix-upedness.

I'd try making sure all traces of java are gone (including the installer files in C:\Windows\Installer [r-klik on the .msi files and select Properties till you find the _05 installer and move or delete it] which is just wasted space at this point, then try the _06 upgrade.