Steve, I have no experience with in-memory databases. Nevertheless I tried setting up the application using Derby in-memory (thanks google) and the bug doesn't show up: it happens with MySQL. I haven't tried other databases.
The datasource is defined in the glassfish-resources.xml file, you can remove the one on the EJB module.
I really have no idea on how to download, install, run, deploy and test the application in glassfish on an automated process, maybe someone can help on that.

I am not an expert on glassfish internals: my uninformed guess is that when a timer executes a different class loader is being used and for some reason the thread cannot access the driver class...? Perhaps there is a glassfish expert following this that could help?