Don't think it's an install issue. I've just reproduced it on one of
my stores for you: only seems to apply to zone rates shipping where
changed default values aren't stored. Flat rate shipping doesn't
appear in these settings at all, and other enabled shipping methods
don't have defaults available to change.
I haven't experienced any problems with this although it appears not
to work. I think the merchant calculation is performed before the
order is sent to gc and these settings appear to be needed if gc
doesn't get a reply from your store, so my theory is they belong to an
earler version of gc that worked in a different and more error-prone
way. This is just an uneducated guess, tho