I've recently set my scroll-margin value to >0 and immediately had
problems using Gnus. First, I would recommend to apply the patch that
sets the scroll-margin to zero in summary buffers:

http://article.gmane.org/gmane.emacs.devel/85300

Even if this patch may only cure the symptom of a bug in Emacs I'd still
think it should be applied since a) it does no harm and b) the summary
buffer is otherwise practically unusable if scroll-margin > 0 and
Emacs 22 or newer.

Additionally, I noticed that when I hit ENTER in the summary buffer to
scroll the currently displayed article by one line, it often scrolls by
nearly a full page. This frequently happens in shimbun groups, but not
always - I can't really say why. My guess is this is due to

(move-to-window-line -1) 

in gnus-article-next-page. I fixed this behavior by putting the cursor
in the middle of the article buffer before calling
gnus-article-next-page-1 (see attached patch). This works for me, but I
don't know if this is the correct thing to do. Scrolling in Emacs is a
deep mystery to me...

-David