Ever since Windows Vista, applications that are not running with raised privileges that try to write to the Program Files (or Program Files (x86)) folder will in fact write to the VirtualStore folder, unknowingly.
Microsoft thought that this would be better than a program failure (caused by the access restriction). And indeed, thanks to this, most old programs that save their settings in the Program Files folder will continue to work with Windows Vista+, and each user will get her own settings, as a bonus, even though the original software manufacturer did not think of this.