I had a similar problem. I bought the Ion Pro RT / Ion Flare RT a couple weeks ago to put on my urban bike, which has my Edge 25 attached. The Bontrager owners manual indicates that the lights come with ANT+ and Bluetooth enabled. As long as this is enabled you will have the challenges described above. I don't think there is any value controlling the Bontrager lights via the Edge 25. Too slow and the lights do not turn on in the mode I like. The easy solution is just to disable ANT+ / Bluetooth on the lights. I followed the Bontrager owners manual as follows:
"To disable, with the light off, press and hold the power button for 5 seconds. The main LED will flash once at 8 seconds, and again at 15 second. Release the button after the second flash"
I did this and the lights are completely unpaired from the Edge 25. Works fine!
Exact same with me. Except it's my wife's Bontrager light for her bike. Whenever we ride together (often) the Garmin display would shut down if I said "no" pairing her light and my Garmin. So I finally gave up and said "ok". Now whenever my Garmin is on and my wife's light is nearby - like when they are charging - my Garmin turns on her light, and it won't go off no matter how many times you push the button. I have to shut down my Garmin to turn off her light! Stupid!! It is really no hardship to turn the light on/off by pressing the buttons on it. Has Garmin published a solution to this?