This line "Exception message: javax.naming.NameNotFoundException: ConnectionFactory not found" seems to indicate that the glassfish installation is broken (or the link from netbeans to glassfish is somehow broken).
I [b]think[/b] from your original post that you have also installed glassfish separately, as well use as part of netbeans, is that correct? If so, they might be interfering with each other.
Or were you saying that glassfish starts OK when you start it manually, not via netbeans?
Personally, I would uninstall everything then download and install separate, standalone copies of glassfish and netbeans, and make sure that each works independently. Then I would add glassfish to netbeans's list of servers (Service tab in the left panel, right-click Servers, Add Server...).
You could also check the current server configured in netbeans to ensure that everything looks OK, although I wouldn't really know what to look for. You could try removing the configured server from netbeans then re-adding it and hope that it gets it right this time :-)
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