Swiftkey have this issue on their FAQ's
Here are the highlights.
Due to how Samsung handle purchased apps, you are suffering from this issue.
Purchased apps on "some" (but probably all) Samsung phones, have info stored in a folder called /sbin/
This folder does not have sufficient privileges OR the android boot sequence does not know to look there for 'some' default apps. Hense why you lose the default setting and android reverts back to the old Samsung keyboard.
There is however a fix (kind of) ***at your own risk***
I have read that deleting the original Samsung keyboard on ROOTED phones will force Swiftkey to become default, but obviously, upon booting the phone this may take a few more seconds to take effect (by the time you have input your PIN's and the UI has finished loading etc, Android should have set Swiftkey to default, or it might not happen until you actually "need" a keyboard, for instance, after loading your sms app and go to reply to text.
Hope this helps.