While helping out a customer a few weeks ago, we discovered that the .NET Framework cleanup tool and the .NET Framework setup verification tool were not correctly opening, reading from or deleting 32-bit registry values on 64-bit versions of Windows (that is, registry values located under HKEY_LOCAL_MACHINE\Software\Wow6432Node for example).
As a result, the cleanup tool would leave behind some 32-bit registry values on 64-bit systems that could confuse the .NET Framework setup programs when they were run later on. Also, the .NET Framework verification tool would skip checking all 32-bit registry values that it was supposed to check on 64-bit OS's, and that could cause it to report successful installs even in cases where important registry keys/values were missing from the system or had incorrect data in them.
Over the Thanksgiving holiday, I updated both the cleanup tool and the verification tool with fixes to allow them to correctly handle 32-bit registry values on 64-bit OS's. These changes should not result in any behavior changes when running either of these tools on 32-bit OS's.
If you previously ran into any issues with either of these tools on a 64-bit OS, I encourage you to download the updated versions and try them again. Please let me know if you run into any problems with either of these tools.
For reference, here is additional information about these tools, including download links where you can get the latest versions of each of them: