The Advanced Preferences dialog shows the BOINC defaults modified by the override file, instead of the working preferences (defaults modified by global prefs modified by the overrides).
This is highly confusing since it lies about the current preferences - so I've flagged it as critical.
Also, what happened to the preference mask? The original behaviour of the dialog preferences was only to save values that differed from the global preferences. Now, it appears that all the preferences are saved in the state shown by the dialog (which can have unforeseen side effects due to the bug above).