OK-it's been a year and I'm sure you;re merrily chugging along with Shake, but I have the same issue, so I'll post my findings:
I had the time to set up a scene where I placed a 10X10 cube at Zero. Put a checkerboard texture on it, and moved a camera (35mm full aperture, vertical fit) in X while rotating in Y. Baked the camera and exported it. Rendered out images of the checkerboard cube and pulled all of that into After Effects. Created a Solid plane 10X10 and placed it at 0, 0, -5 so that it would match the front plane of the cube. This is the result I got:
http://lh4.ggpht.com/chris.dinardo/SL2uMWr...1280/offset.jpg
As you can see it does not match. The movement of the camera matches exactly, but it is offset.
By (first removing the keyframes) adjusting the zoom of the camera I manually got a perfect fit:
http://lh3.ggpht.com/chris.dinardo/SL2uMlA...280/matched.jpg
This is not an optimal solution, but it works. Can someone please post an explanation of the relationship between the cameras of the two programs? I noticed that after effects has a single value for the film size-is this a diagonal measurement? Is there some way to correlate the values of these two cameras?
Some other interesting notes:
After Effects Z zpace is inverted from Maya (note the Solid is at -5, but the face of the cube would be at positive 5)
A direct import of the camera consistently added rotation to the Y and Z channels (7.4 degrees-pretty considerable)
The values of the camera remain the same regardless of the units of measurement you set in Maya's Preferences (yes I rebuilt the scene at mm, cm, m, in, ft.) A 10 is a 10, so to speak.
MoCon scripts do not faithfully export the same camera from After Effects (adding minute-and possibly negligible-values to the keyframes.)
Also taking the camera from Maya into After Effects, back into Maya and then BACK into After Effects resulted with this:
http://lh6.ggpht.com/chris.dinardo/SL2xO3u...s1280/mocon.jpg
While the Zoom values remained the same, the film size and focal length changed.
Hope this helps, and hope someone can put out some information to explain/help solve the issue that exists.
PPS: I had tried this same experiment many versions ago (like 6.5) and as long as the camera was not Maya's default AE would track spot-on.