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!