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If you can, it would be for the SD card notification. When you start up the droid, that's what the sound is for, it's preparing the SD card. If you go into settings, then sound and display, uncheck SD card notifications and you won't hear the sound. So, if missed call can change the SD card notification sound, that's what I'd try.
Only thing I might wonder about though is if the sound plays before Missed call loads. I'm not sure if it changes a system setting, or if it intercepts the signal to play a given notification and instead plays what you've selected. Anyway, only way to know is to give it a try