I'm also hearing these "beeps" coming from the system. They seem to come at random, I've noticed on "EL MSU P" TG305. They're not station IDs, and they don't sound like tx termination sounds you would hear if you were just listening to a control channel without trunking. And I don't think they are TOT warning sounds, because I've never heard anyone talking before the beeps. Just some weird system beep I guess?
/EDIT
Alright, now that I've been monitoring for a while, I beleive that they are infact TOT (Time Out Timer) alert tones. Open mics that are held open too long are automatically terminated by the user's radio after a pre-determined amount of transmission time. These beeps are "pre-TOT warning tones", notifying the user that they only have about 5 seconds of talktime left before they must re-transmit. Usually when I've heard these tones, however, I've never heard any voice. Perhaps the mic switches are extremely sensitive, or the radio failed to drop the system after the user released the mic? Dunno, but I hope that helps.