You are only partially correct.
While I am dealing with different hardware and operating systems, the application being run, Powerpoint, is the latest available from Microsoft for each platform (and are otherwise functionally very similar).
But this problem existed prior to these version of Powerpoint as well.
I can play every single media file on the Windows machine just fine - as long as it isn't within a Powerpoint presentation. So this is in no-way a hardware issue, nor an OS issue. This is 100% a functional problem with Microsoft and their Office applications. For whatever reason, MS has CHOSEN to support only a very limited list of media types in Powerpoint for Windows, but doesn't seem to mind supporting a much more extensive list on the Macintosh platform.
Functionally yes, but the software is still different for each operating system at the point where it communicates with hardware devices like audio and video. Also, the audio and video devices are different for each machine.
I used to deal with the same issues when I had a Mac and a PC, and I know how frustrating it is.
Apple Macs went to the Intel processor a few years ago, and now I have a single laptop machine: Macbook Pro 17", and I can run both OS X and Windows (in a virtual machine) when necessary.