The extension fence is adjustable, so you can't use it as an absolute reference point. Also, even though theoretically the short adjustable fences should be perfectly in line with each other I have not found that to always be the case. The following procedure produces cuts that many of our customers claim are the best they've ever seen. It uses the simple principle that two 45° angles make a 90.
(first, make sure your blades are properly sharpened and the locking bar is holding at the last position).
Use a piece of 1 x 4 or other similarly wide and flat stock. It does need to be perfectly straight, flat and of consistant width. Cut both ends of a short piece (maybe 6-8" tip to tip) on the same side of the chopper. That is, cut one end, flip it end-for-end and cut the other end so that both ends of the piece are cut using the same knife and fence. Put the 45° angles against a regular square and keep adjusting that fence until you get it perfect.
Then do the same thing with the second side.
As a test, cut four pieces the normal way (right cut on left side of chopper, left cut on right side of chopper) and hold together. It should be perfect.