I almost wonder if there is an activation timeout for third party keyboards. In other words, if a keyboard's process doesn't finish loading in X amount of time or doesn't respond right away, Apple loads the default instead of making you wait a long time or giving you a text field and no keyboard. It's just the type of thing I can see them doing. I've noticed the reversion to default most often occurs when I haven't used any keyboard in some time. Maybe the timeout is too low, or the current versions of third-party keyboards just aren't optimized enough.
It's a shame, as I have really taken to SwiftKey. Same layout as Apple's keyboard, but with drastically better suggestions. Suggestions also appear even when a text field (spotlight for instance) doesn't enable autocomplete (they just don't swap in unless you tap them.)