In late January, when this issue was discovered a fix was published and sent out via Windows Update. This has solved many of the issues customers were experiencing. If you missed the WU fix, you can download it here: http://support.microsoft.com/kb/931573. This is addressing a lot of the issues customers are having, however, we realize there are a few programs that are not covered with this fix and our team is working to handle these as soon as possible.
This issue highlights the importance of the new tamper detection technology enabled by the Software Protection Platform in Windows Vista. When evidence of system tampering is detected the system will go into a non-genuine or tampered state depending on the tamper. Also, depending on the severity of tampering the remedies for it can range from a simple reboot all the way to a complete re-install. In this particular case, the programs in question delete a specific system setting that triggers the tamper detection. This can be fixed by visiting the KB article above and following the steps. In some cases this type of tamper could also be caused by deliberate tampering with core system components. While the current examples are unintentional and we've provided fixes, it is important to have these checks built into the system because it helps to ensure the integrity of the Windows system in turn protecting our customers and our IP.