Well when i used to turn off my cx-9 i used to get a message on the clock display that said goodbye. I no longer get that message. I don't remember if it was also audio. I am wondering if it's related to the bluetooth since that works sporadically. I was going to try to disassemble the steering wheel controls to see if the contacts were dirty where the phone button is but it's not worth it and i could possibly do some damage elsewhere. I guess what i'm saying is if it's not affecting the car don't mess with it.
I was thinking the same thing. Seems to come on when I jump in while the car is running and whip it into drive. No visual display. Going to try to keep track of what's happening when this chime appears.
Do you have navigation (gps) ? I don’t know about the first gen cx-9, but I had a gps before that had alerts activated for speed camera and other things like that. it would do a chime when approaching them. I think some phone applications can produce alerts like that as well.
My Google Maps application does a quick 3-bell chime when I'm approaching a speed trap. It only does that when I'm actually navigating somewhere though. Maybe your TomTom does whether you're navigating or not?