The /configuration/config.ini file should contain org.eclipse.core.runtime@start in the commaseparated osgi.bundles property. Here is the default osgi.bundles property, maybe it was (accidently) changed during some upgrade:
osgi.bundles=org.eclipse.equinox.common@2:start,org.eclipse.update.configurator@3:start,org.eclipse.core.runtime@start
You can if necessary override it by setting it as VM argument in /eclipse.ini:
-Dosgi.bundles=org.eclipse.equinox.common@2:start,org.eclipse.update.configurator@3:start,org.eclipse.core.runtime@start