On all my systems where v3.2.4 is installed, the installation is put into a Sun directory/folder. Not an Oracle one. There are no Oracle directories/folders
on any of my systems.
If you're doing an upgrade the installation directory won't change. A clean installation will use the new default install location.
I also wouldn't put any faith in System Restore; it's a very crude tool.
You can also quite happily create new machines in VMware Player, you just need the vmx config file which the software won't give you the option to create. These can be acquired from numerous websites.
I'd be tempted to temporarily disable the Windows Installer service and see if that prevents the mystery deinstalls. MSI is a great idea on paper, but the implementation is prone to all sorts of strange issues such as this. Don't be confused by the installer being an EXE, it's just a wrapper for the MSI.