SwiftKey gets removed as input method after every update
Seems to be a Google issue. There is a blog post on SwiftKey's support site. 

Essentially:


  The issue is that Google Play installs paid apps in a particular location on your phone and that in some versions of Android (particularly 4.1 on Samsung devices) this location is not available at the point in the boot process where keyboards are being switched on. So your phone does not know that you have SwiftKey, and it defaults back to the phone’s keyboard.