I have the exact same thing happening and it's been a huge problem for me. I upload lots of videos for my business and Safari can't play half of them.
Apple, if you guys read this stuff - I got my first break in commercial art when Apple was starting to gain momentum in the print graphics industry... 1989-1990. I was illustrating and doing PASTE-UP at the time. Today, most of my work is agency-based so I hope you can appreciate my observations.
I have been dealing with these software farts with more frequency than ever before. And it's getting worse. I believe Apple's balance between the mobile market and the desktop market is way off.
Now, with this bug, I'm going to have to go to FireFox or Chrome. I really don't want to do that because their UI is not as good as Safari's but I don't know what else to do.