This problem appears only in chrome and safari, firefox works well. I'm using browser object "Is downloading update" and "On update ready" to force update on the client. It's weird, but the first time the page is being loaded "On update ready" is not trigered. After you refreshed the page and uploaded a new update it works.
And yes, I upload all game files including "offline.appcache"
I think I even saw this behavior on some game on Scirra Arcade. The guy wrote in the description "If you stuck on downloading update, please refresh the page."
Any ideas how to fix it?