Well, I fixed showflat. [:"red"] Could someone please verify this is correct. [/]
Open showflat.php
Change
elseif ( ($PostStatus == "Moderator") && (stristr($modlist,",$Username,")) ) {
to
elseif ($PostStatus == "Moderator") {
I am not sure what
&& (stristr($modlist,",$Username,"))
is supposed to do, but taking it out seems to fix the problem with mod flags not showing in flat posts.