Cairo-dock, the graphical shell I use on the concerned computer is shown over the window while playing on the snapshot, when Minecraft is in focus, which obscures the hotbar, and everything on the lower window if Minecraft is maximised.

This did not occur in 1.5.1 (As you can see in the third screenshot. The same is also true in 1.5.2), Where Cairo-dock is correctly hidden behind the game window when the Minecraft window is over it, this is also true in fullscreen.

LWJGL is the same on both versions, as you can see in the second two screenshots, so this is not the issue, as has been previously suggested.

Steps to Reproduce:
1. Start launcher (new dev launcher, not old) by locating it and right clicking, selecting Oracle Java.
2. Select relevant snapshot.
3. click 'Play'.
4. Maximise window if not already (but not F11 fullscreen, the problem does not occur then).
5. The issue becomes apparent: exactly as it appears in the screenshot of the snapshot, cairo-dock is shown over the lower part of the game, when the game is in focus, and the window area is over the dock.

To summarise
Torabi sums it up very well (far better than I can, at any rate):

So, to summarize: The Minecraft window should cover (be on top of) the dock when the Minecraft window has focus. This is the behavior it had in 1.5.1.
The problem being experienced is that the dock is always on top of the Minecraft window, regardless of focus.

Screenshots

1. (2013-04-25 18_27_27) Screenshot In snapshot with issue
2. (2013-04-25 20_31_19) Screenshot showing the version of LWJGL for the snapshot
3. (2013-04-25 20_33_01) Screenshot showing version of LWJGL in 1.5.1, and that the issue does not occur in 1.5.1

Edited to clarify many points, thanks, Torabi