I have two displays. Playing on a laptop, with an external monitor. The external is configured to be on the left side of the laptop, with the bottom of the laptop screen and the bottom of the external flush. The laptop's screen, in pixels, is slightly shorter than the monitor's. When playing Minecraft maximized (not fullscreened) on the external monitor, clicks are not being detected properly.

Any click on the lower 2/3's of the monitor seems to work just fine. Any click on the upper third appears to happen as if I was clicking right on the 2/3-ish boundary (e.g., as I move my mouse upwards, the click's y values get clipped or clamped at some y value).

The exact cutoff seems to be where the top of my laptop screen is. Anything above that is just clipped. If we assume the top-left of my laptop is 0,0, and y increases down, x increases right (typical programmer axis), then my left external monitor is at, say, -1000,-300. (I'm making the numbers up.) Every click at click_y < 0 seems to occur at click_x,0

Even if I make the top of the external and the laptop flush, I get the same behavior. e.g., if my laptop is once again 0,0 in the top left, then my monitor is at -1000,0, but no change. (i.e., the "working area" hasn't shifted up.)

This person also seems to be experiencing this:
http://www.minecraftforum.net/topic/1506917-creative-mode-bug-cant-click-tabs/

Her example is a good one: she can't click the creative mode tabs. Neither can I. Now, the creative mode dialog resizes itself (in terms of pixels) depending on how tall and wide your screen is. If we call the smallest size of this dialog "Size 1", then my dialog is Size 4. (e.g., each "faux pixel" in the dialog is 4x4 pixels. the dialog is zoomed by a factor of 4.)