It's probably not been addressed because it's hard to fix something that can't be seen. I can give an explanation of a problem here, but if a programmer isn't seeing it, then there's a loooong process of determining what's different between my system and their test system. At one point, it was determined that an OS upgrade/Keynote version combination caused a specific problem that couldn't be seen otherwise. Once that was known, the problem was able to be fixed.
For example, let's try to re-create the issue in a controlled way. Create a presentation now with three slides. Put some Myriad text on each slide, something like Slide One, Slide Two, Slide Three, then save the file and archive a copy (right click and choose create archive of...).
Then, open the original immediately and see if anything has changed. Then open it tomorrow. If it still looks the same tomorrow, leave it for a few days and try re-opening it. If you see the problem, double click on the archived copy and try opening it. If the "protected" version has the same problem, then you more than likely have some systemic problem. If the "protected" one opens up as you originally left it, then there's some weird stuff going on. 🙂
The systemic problem means try things like creating files under a different user, save to a different drive, things like that. However, if the files are actually different, well, I don't think I'd know where to start then!