Best described as a step by step (I hope):

1) use xchat with:
  -tabs, instead of tree as channel
  -tabs at the bottom
  -the tray icon enabled
2) hide xchat (through the tray icon, or simply by clicking the X on the
   title bar)
3) do stuff
4) move mouse to lower right corner, click xchat icon to unhide
5) move mouse to the left, without moving it up to choose a channel to
   say something in, cannot click because the shadow drawn at the bottom by
   the message tray, is not just a shadow but also catches clicks

This happens to be my step-by-step, which is rather specific, but the problem is more generic IMHO, if one does something with the message tray and then wants to click something at the bottom of the screen this fails because the "shadow" catches all clicks.

Possible solutions:
1) Only make the area of the message tray which has icons actually catch clicks, and make the rest of it pass through clicks to whatever is underneath it. The visual concept of a shadow also sort of makes one expect this, like with the shadows cast by windows on lower stacked windows, unlike the tray message shadow these do not catch clicks. This IMHO is by far the preferred solution.

2) If 1. is hard to do, maybe hide the message tray not only when the cursor goes above a certain height, but also when it is more then X pixels to the left of the most left "tray-icon"