You need to make the extensions show in Windows, NOT in iTunes (unless I am misunderstanding what you are saying). It sounds like you are saying that when you locate the file on your computer in Windows Explorer the file extensions are not showing, but if you look in iTunes you can see the file extension. 
If you're saying your file does not look like that when you locate it in Windows Explorer then you need to have your setting in the Windows folder to show file extensions. If you are seeing the extensions but you're trying to figure out how to actually change them, all you have to do is click on the file name as if you are trying to edit the name. Once the box opens to allow you to type in it, just go to the extension (in the pic I posted it's .mp3) and change it to .m4r. When you click "enter" a dialog box will pop up with asking if you sure you want to change it. Select "yes". Double click on it and it will start playing in iTunes. It should show in the Ringtones folder.
I admit I am getting a bit confused by the thread so you may have said that the tones are already showing in iTunes in the ringtone folder but they don't show on your iPhone. When you try to sync them, if they are too long then they will not sync to the iPhone. You will need to adjust the length of the tones.
If none of this is your issue then I apologize. If there is really an issue with your iPhone then it should be replaced under warranty. Not sure if the issue would be your iPhone or your computer. You could always try to uninstall iTunes and then re-install it to see if that is the issue but I'm not so sure that's what the problem is.
Sorry if the screen capture is too small...not sure why it came out so small.
