The GPE has been pretty buggy over its lifetime, particularly wrt the HRD config.
To fix your problem (and other problems relating to GPE run/debug) configs:
If you open up your project properties and navigate to
Google -> App Engine
As well as ticking 'Use Google App Engine', make sure 'Enable local HRD support' is ticked too.
If this box is greyed out (i.e. disabled) and unticked, you'll have to work around it. You can do this by opening up <project>/.settings/com.google.appengine.eclipse.core.prefs in an editor, and change the property 'gaeHrdEnabled' to true
To set the unapplied job percentage, in your run/debug config, use the tab 'App Engine'. If you need to hack around this not working, then setting '-Ddatastore.default_high_rep_job_policy_unapplied_job_pct=50' in your run/debug VM arguments will work.
Im not sure what all the triggers are, but when you make changes in the GPE preferences panel, the App Engine tab in run/config and some other places the run configuration is automatically updated.
This is why even when you add unnapplied job policy manually, it gets removed. This is a worse issue when other plugins want to modify your run config as well (for example, with jrebel they have a contest to see who can add the most javaagents).
The best workaround we've found for this is to get your run/debug config as you wish it, the on the 'Common' tab, choose Shared file. You can then make the file read-only on the file system which will prevent any plugins (GPE, JRebel, anything else) from undoing your changes.