In after effect, in my experience, I make the Z depth channel either a separate pass altogether, OR I render my objects with a depth shader giving me more render options.

Then in AE, I import that sequence as another piece of footage, and add it to the stack as another layer, but "POINT" to it for depth blur effects, fog etc.

So basicly, don't include the Z channel in your main RGB render from Maya.
Render it as its' own sequence from Maya in either of the 2 ways above, as currently for AE 5 and 5.5, it does not notice the Z channel in an .iff file.

AE 6 may have updated this.

Does that help?