It seems like what you’re experiencing is that the data on your host doesn’t look like what you expect it to. So the first instinct is to check for caching – something that’s getting in between your web browser and what’s on your host.
It looks like you’re using CloudFlare. That is exactly such a thing that could cause problems.
I don’t know that CloudFlare is the root of the problem (it probably isn’t) – but it will definitely prevent us from seeing the actual files on your server – as it will be trying to cache things.
I would recommend completely disabling cloud flare and any other caching or distribution services – at least until we get all the problems resolved. Once we get things working smoothly, then you can worry about speeding it up with CloudFlare.