Nice one.
The cause was the old F-15 SMTD mod I had sitting in the \Saved Games\DCS\Mods\aircraft folder.
Strange as you'd think if anything the mod would be the thing affected by the vanilla FC3 F-15C textures. I'm not sure why it cross-pollinated it's textures into the stock F-15C but I really don't know the nitty gritty of the DCS file structure.
Hopefully this thread helps someone else if they have the same issue.
The Oligopolist's post in Streaky, cloudy texture on instrument glass after cockpit refresh was marked as the answer