My son has a bunch of light systems on his bike he can control from his Garmin Edge 1030plus and previously with a Edge 820. Sometimes he'd have issues similar to yours but not all the time. Frequently they seemed to either be after a software update or when he hadn't ridden the bike in several weeks. For times he rode 3 or 4 times a week it usually wasn't a issue.
However out of all the issues one can have with their Garmin, this seems to be the one that remains a issue for many. Though it has been a while since someone here has brought it up.