Here's the reply I got from SwiftKey support. May be useful to others.
Google have made a change to their code that means that every time you reboot SwiftKey is deactivated and switched off. When the reboot happens none of our code is running, so there is no change that we can make that would have any effect.
Google did not intend for this to happen, and they have fixed it in a later version, but unfortunately it does often take a while for the updates to get around to everyone.
You can find a fuller explanation here http://support.swiftkey.net/knowledgebase/articles/122554-default-keyboard-reset-on-every-restart-or-reboot-
Right now the only choices are:
1 - continue to use SwiftKey (and turn it on every time you reboot your phone - if you place the SwiftKey icon on your home screen this will only take two clicks)
2 - use another keyboard until it is fixed, then switch back to SwiftKey when you get the update
3 - we can refund you for SwiftKey
Sorry we can't be more help,
Needless to say I didn't accept their kind refund offer. It's a great app.
I'll try uninstalling /reinstalling SwiftKey but will probably just stick it out. I'll also check that Greenify is not hibernating SwiftKey without my knowing it.