The FiltersConfigurationDialog has a 'Restore Defaults' button to restore the dialog to its default state.

If USE_MARKER_LIMITS preference is false then 'items per group' is restored to 1000.
int markerLimits = useMarkerLimits ? preferenceStore.getInt(IDEInternalPreferences.MARKER_LIMITS_VALUE) : 1000;
This is in contrast to the default value for 'items per group' of 100 when Eclipse is first launched.
node.putInt(IDEInternalPreferences.MARKER_LIMITS_VALUE, 100);
The restore default button should restore the 'items per group' to the same value as on first launch.
- note : this issue is not normally reproducible in Eclipse as USE_MARKER_LIMITS preference is true by default.
It can be seen when USE_MARKER_LIMITS preference is being set to false via plugin_customization.ini for example.