I've made a quick video to demonstrate the problem, as it's easier to show than to explain:
Premiere Pro Problem - YouTube
This problem happens at random. The only way I've found to recover is to grab an old copy from a backup or rebuild the composition. I've had to resort to keeping each short video in a separate project, because every time I open a project i'm afraid this will happen. It seems to happen both on my work and home computer, and has been happening since before the recent update.
Like I said, I couldn't find any mention of this problem online, but I might just be looking under the wrong keywords.
Any ideas?