The iPhone OS templates can be found at
/Developer/Platforms/iPhoneOS.platform/Developer/Library/Xcode/Project Templates by default, while the Mac OS X project templates can be found at
Are there any folders/files in the folder containing the iPhone OS templates and/or are they a duplicate of the Mac OS X project template folder?
One option you can try is re-install the iPhone SDK (if necessary delete the
/Developer folder if you want to start fresh), the other would be to restore the iPhone OS Project Template folder from a backup.