your config.ini should instead of listing all required plugins only rely
on org.eclipse.update.configurator, i think.
this is normally achieved by modifiying the launch-configuration of your
product:
in the tab "configuration" check in group "Configuration file" "generate
a config.ini with default content".
maybe you have to switch in tab "Plugin" from "launch with all workspace
and enabled external plugins" to the second or third option, too?