When I increase the default font size (say, from Menlo 12 to 14), either by Options->Set Default Font or by
(set-face-attribute 'default nil :height 140), the top of the buffer becomes hidden. The visible part of the buffer starts a few lines down (depending on font size) and the actual top is hidden above the top of the window. I can move the cursor up to the top of the buffer, but it disappears above the window.
M-x beginning-of-buffer doesn't help. If I lower the font size, it becomes visible again.
Emacs 24.5 (9.0) on OS X Yosemite (10.10.5)