On a reboot, is your custom keyboard (i.e. SwiftKey) not being remembered as your default keyboard?
This application fixes this problem in a roundabout way. After you reboot and launch your first application, you'll see the dialog that lets you choose which keyboard you'd like to keep for the duration of the boot. Once you reboot, it'll ask you again.
The Android OS prohibits applications from changing keyboards behind the scenes - and since Google is too lazy to fix this problem, this is the best workaround available.
It's frustrating when you reboot, then start to write a text and realize Android has reverted your keyboard to the stock keyboard.
It's been reported this is an issue on most Samsung devices running the 4.1.1 and 4.1.2 Jelly Bean OS.