Hi brain
What ver of logix are you using as I set one up In ver 20 and it's easier than ver 18 which the last one I did which to be fair was not to bad.
I download a white paper from cognex web site that should the mapping when it's set up as you have said.
A few things to watch out for are
The vision done bit goes high when the first picture is finished and the results are updated then after you trigger the camera again the bit goes low and then high after the next trigger and so on.
If you get two pass or fail results in a row the bits do not change status, in other words they not clear after you give a trigger as I taught the would.
Are you selecting jobs from the plc?
Drop me a line if you can't find the white paper if you are using less than ver 20 of logix
Donnchadh