im having this keybind reset/loss on my all toons also and it doesnt matter if i use character specific or account wide bindings they reset/lose bindings and usually it happens when im using vehicles/mounts with (vehicle) bar, after i jump out from vehicle/mount my bindings are gone for good. sometimes it happens also when i log in and bindings are gone.
hopefully you are able to find this bug or blizz (mess code)
and you are able to fix it.
good work anyways with your UI addon, its a piece of art