I think we have a similar problem:
My HTML5 Application Cache Manifest is caching everything
I haven't found the ultimate answer but from what I've learned it seems that the manifest is not meant to be set on every page. Again I'm not sure but this is a hack that I came across. I have a page such as manifest.html that has the
<html manifest="manifest.appcache">
I learned that pages which do not have this will not be added to the cache however they will still continue using the application cache if on the same domain. Therfore if you include manifest.html a plain html page that has this in an iframe on everypage it will not cache that page like chrome will no longer output:
Adding master entry to Application Cache with manifest
but if you go to network tab you will see that it is using the cache
so basically instead of manifest attribute on html tag put this in the beginning of body:
<iframe id='manifest_iframe_hack' style='display: none;' src='temporary_manifest_hack.html'>
content of temporary_manifest_hack.html:
<!DOCTYPE HTML>
<html lang="en" id="sexxymofo" class="no-js" manifest="manifest.appcache">
<head>
<meta charset="utf-8">
<title>Hack 4 Manifest</title>
</head>
<body></body>
</html>
now since you didn't specify your problem specifically I am worried you might have an issue with a valid manifest, keep in mind there is no wildcards in the manifest, use this url to validate:
http://manifest-validator.com/validate
the simplest error will cause the manifest to be invalid and no appcache will be used, use chrome
for debugging as the console will log every step of the process, also see this url in chrome:
chrome://appcache-internals/
Again take a look at my question in the answer above to learn more