Since Windows Vista, the program files folder as well as a few others are never localized and always named in English, no matter the OS language. XP and earlier did name some folders according its language, but newer versions throw away that.
What you're seeing is a problem in Windows Explorer, when it says "Programske datoteke (x86)", Explorer is lying to you, the folder is not really named like that. Explorer uses those pesky "desktop.ini" files to control such things and show a more "friendly" name instead of the real one, among other things.
You can confirm in command line or by using a more serious file manager that the folders are in fact called "program files" and "program files (x86)".
If you really want that misbehavior, just copy the desktop.ini over, it's likely to be missing in one of them.