Well, not really knowing anything about this issue, I'll just as a couple of stupid questions. :biggrin:
Are the two sound files named the same? Have you tried selecting a different sound file all together and then going back to the one you want? In other words, deselect everything and then select some weird one you've never used. Use it for a little while and go back and deselect it and then select the one you actually want.
Good luck.
Also, check and see if the system has one notification sound selected (menu/settings/sounds) and the app has a notification sound selection too.