John,
By default, the installer runs in 32-bit mode on 64-bit systems and if you install a 32-bit application, your files go into "Program Files (x86)\MySubfolder". If your application is native 64-bit, then you have to run the installer in 64-bit mode to install your 64-bit files to "Program Files\MySubfolder".
IMPORTANT: Only native 64-bit applications go into "Program Files" on x64 systems!!!! You never install 32-bit application into this folder.
See attached screenshot.
Does this help?
Friedrich