It appears to stem from this change:
1998-09-22 Hrvoje Niksic <hniksic(a)srce.hr>
* isearch-mode.el (isearch-mode): Use overriding-local-map to set
the keymap, not minor-mode-map-alist.
(isearch-done): Restore overriding-local-map.
What's happening is in Gnus summary mode I used to be able to isearch
for a group and then hit M-g to fetch new mail in it. In 21.2 this
instead runs the unbound (in Gnus) `goto-line' command.
I prefer the 21.0 behavior.