So my iPhone 4S's keyboard shortcuts stopped working in iOS 6. By stopped working, I mean I can't seem to create new shortcuts, or delete existing ones. Also, those created on my iPad don't sync with my iPhone. The fix is strange:
After this, the shortcuts I previously created during the bug showed up and the shortcuts I deleted disappeared. They also successfully synced via iCloud onto my iPad almost immediately.
That's a strange way to fix this bug. In fact, that's the strangest bug-fix I've ever encountered.