I had the exact same problem when trying to upgrade, it was because I had skipped one patch, and the version I was trying to upgrade was too old for the last patch (the previous patch has made some serious changes in the files structure and registry)
Luckily for me, even if I had not installed the previous patch, I had already downloaded it, so I first updated my version with it and then the beta 3 installed without problem.
At worst, just download the full beta again in order to have the latest version.
@Stardock: you should maybe implement a simple version check when running a patch so the user get an appropriate error message instead of the current one.