It’s possible something is filtering your content on initial upload only (but you say it’s not a plugin) — perhaps something in your theme? You might try switching briefly to the default theme and see if it’s also a problem there.
Outside of that, I’m out of ideas short of viewing the problem first hand.
– Disable all the plugins
– Upgrade your wordpress version to the latest version
– Assign 755 recursive permissions to wp-content folder.
– Remove all unwantec code from htaccess
– Check with default theme in order to ruled out theme level issue.