Thought I'd bring this up again as I still don't have a really good solution. I don't know what Sleeper actually does but when the timer runs out and an SMS is received the N900 also just plays back the short beep. When I set the mediaplayer on pause manually the configured SMS notification is played though.
Right now I'm using the Canola player that plays the configured SMS sound during playback but I'd prefer the standard mediaplayer.