The sounds selected for the beep are loaded into RAM during startup. It's
possible that your System Folder may be corrupted and is pointing to
another beep sound.
Try starting up from a locked System disk and let it sit for a while to see
if it does random beeps. If this doesn't fix things, trash and reinstall
the System Folder. If the problem still persists when you start from the
floppy, then you may have a hardware failure.
You also mentioned no special CDEVs and INITs being used. Were you
referring to sound-type INITs? Other INITs that have some time/delay
activation might also cause similar symptoms: SuperClock, screen savers,
and spelling checker CDEVs to name a few.