M,
I am preparing a revision to the original blog post that should address your backup issue, among other symptoms already described, that we know and understand. In addition, the exact ETA for the release of the newer version is not known and will be communicated as soon as it is. Our recomendation is to uninstall the rollup.
Robotworx,
The scenario that you describe is handled using the MSI build-in file-in-use detection logic for both the install and the uninstall scenario. Any file being consumed by a thrid-party app will force this to happen since the Rollup does not handle the file-in-use scenario and does not give an option for the user to stop those applications/services manually so the reboot can be avoided. With that said, I am currently having someone look at your scenario in the lab and trying to see if I might have not understood your explanation + expected results.