I agree with Chris- when possible, I prefer a compete wipe of the old app before installing a new one.
Try this to get the old .msi app off your systems:
Find the product code for the old install in the registry.
Run the following command line to uninstall it:
c:\windows\system32\msiexec.exe /X
/QN
Then run your transform install command line.
You can even string them together in a batch file if you want.