I'm having the exact same problem with our AFM. It doesn't happen often, but when it does it really blows your socks off, it's THAT loud.
While discussing this with a friend, it appears he has the exact same problem on his AFM. He also mentioned hearing it from others that this is an issue specifically with AFM. It almost seems to me like this could be a software glitch triggering that 3 second "loud digital noise" occasionally. Or it could be that they used a bad component on the soundboard and that many AFM's around the world are affected.
FYI, my friend and I both have attract mode music turned off on our games, and attract mode sounds turned on (flipper buttons trigger a sound in attract mode). I wondering if that could be related?
Not sure what software version I'm running but fairly sure it's the latest. Will check next Friday.