recentchanges.pm sets the template variable HAS_DIFFURL to 1 based solely on whether or not diffurl is defined. I found that diffurl was defined, but empty. The recentchanges template depends on this for recentchangesdiff to properly function -- diff toggling is dependent on HAS_DIFFURL evaluating to false. Adding a check for a non-zero length diffurl fixed the issue for me. A patch against ikiwiki-3.20121212 is as follows:

--- a/IkiWiki/Plugin/recentchanges.pm   2013-01-27 20:08:59.000000000 -0800
+++ b/IkiWiki/Plugin/recentchanges.pm   2013-01-27 20:08:30.000000000 -0800
@@ -181,7 +181,8 @@ sub store ($$$) {
            else {
                $_->{link} = pagetitle($_->{page});
            }
-           if (defined $_->{diffurl}) {
+           if (defined $_->{diffurl} &&
+               length($_->{diffurl}) > 0) {
                $has_diffurl=1;
            }

(There should be one more line at the bottom with a single space on it...)

applied --Joey