Looks strange. I have tried your file on Mac 10.9.3 with QuickTime player version 10.3 (727.4) as well and found it to be working fine. I have got about 48.9 MB of mov file. Also it was working fine in AME when I converted it to a mp4 format.
Few questions:
In your first post you have mentioned 'On top of that, when Adobe Media Encoder CC opens up it also states there is an error with the file.' I hope it is Adobe Media Encoder CC 2014 and not Adobe Media Encoder CC. Flash CC 2014 can only work with AME CC 2014.
Also the video export depends on QuickTime player. Is there a chance that the installation of QuickTime has any issues. Can you please try uninstalling and re-installing QuickTime and see if that helps?
Thanks!
Mohan