This problem is caused by a bug in the version of Windows Installer that is included with build 1218 of the Windows x64 Edition operating systems. Newer versions of these operating systems, such as build 1247, have a fix for this bug. For this reason, moving to a newer version of the operating system will allow you to install a patch for MKS Toolkit.
Another solution is to do an administrative install and apply the patch to the resulting administrative image. Then install MKS Toolkit from the patched administrative image.
For more information on administrative installations, please see the Installation FAQ.