Seems to be par for the course for the AT&T Note 2 as mine does the same thing on restarts. It's a simple matter to switch it over, but a minor annoyance nonetheless.
It is a bug in Google Play. The best workaround is to uninstall Swiftkey 3, turn off automatic update also. Then download the most current apk and install from the download, not from Play. The keyboard will stay after a restart.