Yes, you've lost some of the Windows files. There are a number related to this so I can't specify which one(s) are affecting your system, but I run a number of my stripped systems deliberately in this way with no Windows setup.
The simplest way to cure this is to do an "install over". Just run an installation over the top from your Windows installation CD and it will make good any lost files for you and return that facility.
Back up your data first as a precaution, but doing this will normally keep your existing programs and configuration intact.