I just ran into this problem and stumbled across a different situation. Although it's probably just a unicorn, I thought I'd lay it out.
I had one session that was smaller, and I noticed that the font sizes were different: the smaller session had the smaller fonts. Apparently, I had changed window font sizes for some reason.
So in OS X, I just did Cmd-+
on the smaller sized session, and it snapped back into place.