v1.8 makes sure that there's always an "accept" key, even if no answers were selected. I'm pretty sure that this should solve the underlying problem here. It's very unlikely that no "accept" options are added when the user selects them – the 2% rate at which this happens would be more consistent with the cases where the user just doesn't select an option (or accidentally unselects). That said, if you can still reproduce the problem in v1.8, let me know.
Did you or the annotator reload the app at any point? If so, it's possible that you end up with one unlabelled batch, since Prodigy has no way of knowing that it's "not coming back". You can find more details and an implementation example of an "infinite stream" here: "No tasks available" on page refresh - #2 by ines