Please keep CCing to 11544@debbugs.gnu.org so the information you
provide does not get lost.

 > On this bug, after typing the ? first the window grows to normal size and
 > then the window's left edge stays in place

But when you type "?" on your Windows Emacs the left edge moves?  Could
you try comparing the return values of the function
`ediff-make-frame-position' on GNU/Linux and Windows respectively?

 > and the width decreases to about
 > a characters width in a fairly continuous movement.

So it looks like an animated variant of bug#11480.

 > I tried emacs 23 and
 > it does the same thing on Ubuntu precise.  I use emacs on windows and have
 > never seen this problem using ediff there if that helps.

I don't have the slightest idea what's going on so I can only suggest to
try the following: Locate the file ediff-wind.el (in the lisp/vc
subdirectory) and try to apply the patch I attached.  At least this way
we should be able to find out whether doing two separate calls of
`modify-frame-parameters' confuses your window manager.

Thanks, martin