On my Soyo MoBo the long beep occurs if the CPU fan is too slow. Since I'm using a Zalman cooler, I disabled the warning so I don't have to hear it all the time (the computer will still boot up though, either way)
Also, if there is data in the boot error log, it will beep.
Maybe your board has something similar.
You may want to boot with the case open and check to make sure all the fans are spinning. If so, maybe you let it boot and see what the post screen is like.
Finally, it is possible the MoBo owners manual will have beep code explanations, so you might find something in there.
-D'oh!