I'm using the Google Plugin for Eclipse, today i encountered a similar
problem and solved it.

opened the debug-level log, if you find the following text, remove the
gae library and re-add it.
DEBUG [org.datanucleus.util.Log4JLogger.debug(Log4JLogger.java:58)]
Class "org.eclipse.core.runtime.RegistryFactory" was not found in the
CLASSPATH [Class resolver called from
org.datanucleus.plugin.PluginRegistryFactory.newInstance (line=89)]
DEBUG [org.datanucleus.util.Log4JLogger.debug(Log4JLogger.java:58)]
Plugin Registry "org.datanucleus.plugin.EclipsePluginRegistry" not
found. Falling back to DataNucleus registry. Reason : Class
"org.eclipse.core.runtime.RegistryFactory" was not found in the
CLASSPATH. Please check your specification and your CLASSPATH..

regards

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