I'd suggest making ez publish your root. Based on the configurations it seems you have currently in the settings it may be looking for the files in the virtual server's root. If this isn't possible due a currently active site in your server root you may want to make a new virtual host like pub.yourdomain.com and put ezpub in there.
I can't say for sure why this fixed our issue, but we have almost the same setup as you mentioned and experienced the same symptoms. Then, when i moved everything to the vhost's root it seemed to go away. Can anyone provide some clarrification on why this is?
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