Half good news, with the OpenFL code added the loader bar is actually moving, meaning that atleast some of the issues were fixed. Bad news is that it still isn't quite enough, there are still issues preventing it from fully loading.
Inspecting with developer tools appears to show the main issue as being unable to load the higher resolution joystick images of all things.
->'[inner/outer]-joystick@[1.5x-4].png:1 Failed to load resource: the server responded with a status of 403 ()'.
I have no idea how or why this is a problem, I guess I can try fiddling with either the scale (it's set to 1x) or the android/ios settings.
There is also a warning about the AudioContext,
->'The AudioContext was not allowed to start. It must be resumed (or created) after a user gesture on the page.'
Probably not important I think but worth noting, I guess.
Also, here's the exact email I was sent for reference:
"Hey there,
Our development team was able to locate the issue of why this might be happening, and what they concluded is that Stencyl has asset caching, which interferes with the urls. For that reason, you'll need to disable that when exporting the build to Game Jolt. "