dmfahey,
It looks like the errors you see are produced by Serena, not by MyEclipse. MyEclipse is using linked folders technology during EJB Deploy operation.
Can you check if the deployment works fine when you uninstall the Serena Dimension plugin ?
I assume Serena does not support linked folders in the projects it tracks, or at least does not support linked folders with regard of the type of repository you are using, so you are getting notification errors regarding that matter as soon as ME creates a linked folder.
Could you please ask Serena support if that is true and Serena does not support linked folders? Also please let them know that a real support is not needed, all we need is the linked folders to be totally ignored.