We’re not sure why “MyEclipse Derby” has disappeared from the startup list, but we’re looking into being able to easily disable it.
As a quick workaround, what you can do now is go to
<installation directory>\configuration\org.eclipse.equinox.simpleconfigurator
and edit the bundles.info file. You will find the following line
com.genuitec.eclipse.derby,11.0.0.me201211281531,plugins/com.genuitec.eclipse.derby_11.0.0.me201211281531.jar,4,false
Simple delete or comment this line and restart MyEclipse. Would recommend making a backup of the file first.
Sorry for the inconvenience caused, we’re looking into it. Please let us know if you see any other issues with MyEclipse 2013.