[Fixed]-Site not serving media files but serving static files correctly

Are you sure /var/www/MySite/media is your media directory?

Maybe you confuse the staticfiles (which are collected by the collectstatic command) with the mediafiles, which are saved by users of the webapp.

Looking at your settings, I believe your apache configuration should serve
PROJECT_ROOT + '/media'.

Or, you change your settings file so that MEDIA_ROOT = /var/www/MySite/media