Basic MSI upgrade issue.

I have a Basic MSI that is basically just a file copy. The input is a click once directory that is added dynamically when built. It looks something like this:
App.Application
publish.html
Application Files (Directory)
|->App_w_x_y_z (where w_x_y_z represents the version).

The MSI runs perfectly fine the first time. I have changed the Package Code, Product Version and recreated the installer (also republished the click once so it is now version w_x_y+1_z). When I run the the new installer it tells me it will upgrade the existing installation (good), goes through the motions, looks like it is working, and tells me it completes successfully.

When I go to the directory I installed to, I don't see any change in any of the files. I tried adding the following to MSI Command-Line Arguments 'REINSTALLMODE=vaums REINSTALL=ALL' but to no avail.

When I do an upgrade the previous version serves no purpose anymore. With that in mind is there a way to do an uninstall first (that is silent to the user), or is there something simple that I am missing? Or a better way to accomplish what I need?

/edit - It is worth noting that the files I am replacing have no File Version attached to them.