Are these real short "chirp" beeps? I just got a 790fx-gd70 and was getting 2 real short chirp beeps before the normal beep. Turns out msi thinks it's a good idea to make the system "chirp" beep for each usb device that you have connected to the motherboard. In my case, the USB keyboard and mouse. Unplug all USB devices, then see how many beeps you get.
i have this too. And i must say i found it really REALLY annoying. Random beeps that kept changing (i have external harddrives) all the time. At first i thought it was broken or something. i hope msi doesn't keep doing this on their new mobos