I'm suffering the same problem. It's definitely a bug in the resource handler, because even when I've updated the file, and it's the new file in the deploy directory, the response headers have an old "Last-Modified" header.
It got the correct on shift-reload, but the modified date is still wrong. If it cannot figure out the timestamp from the OS, it's pretty hopeless to use the resource tags.
I'm using NetBeans 6.8 and GlassFish 3, and it's the same problems on both JavaScript and CSS, and I attribute it to the cache response headers of the resource injection servlet (/javax.faces.resource/).
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