Messages just has all kinds of unique weirdness. For instance, the issue where the system randomly reverts back to the Apple keyboard seems to be pretty much fixed in 8.1 except for Messages. It happens all the time in Messages, and it will happen for individual people. As in, if I'm talking to one person it always brings up the Apple keyboard, but if I message a different person it will bring up the third-party keyboard. To fix it, I have to go and change it back to the third-party keyboard for each specific conversation where this is happening. This seems to mostly happen if you tap a notification to go to a message thread.
Fortunately, this behavior seems limited to the Messages app, and even when Messages has reverted to the Apple keyboard, other apps still show the right one (in 8.0.2 the reversion seemed to be system-wide when it happened.)