This actually led me to another solution...though it has similar requirements.
I didn't really want to uninstall and install from .apk - I believe you would lose your learned personalizations and it would lose the Play Store connect i.e. no updates.
I instead chose to try using Titanium Backup to FREEZE both Samsung Keyboard and Swype (since you can't disable them). So far it seems that this fixes it for me.
The problem is that when the phone boots up, Swiftkey is not yet available to the system (as a 3rd party app) when the default keyboard is chosen. It then defaults back to Samsung Keyboard. If you freeze both Samsung Keyboard and Swype, I presume it finds no keyboards available and sets nothing as default...and then when Swiftkey becomes available a few moments later it goes AHA there's a keyboard, default! At least that's how I imagine it lol.