I'm going to answer my own question. It turns out there were two issues. I set the Image Display property to "Partial" because my flow uses several embedded data flows and they were being displayed over other parts of the job. It seems the auto document feature needs the Image Display Property set to "Whole" for conditionals to be properly displayed.
Problem #2 is my job uses a lot of conditional logic and they way SAP has decided to display conditionals is to overlay them on the main image. This would seem to render auto documentation useless for job that contains even moderate conditional logic. When Image Display is set to "Whole" and you have a lot of sub-components it will display the message "The system will only display part of the job information automatically as the whole image is too big and can't be displayed." It would be nice if SAP wouldn't overlay sub components because it looks terrible and you pretty much need to lay your objects on the canvas knowing where the auto doc feature will overlay the sub-components, otherwise you'll have overlap. Again, seems like a very poor choice to me. Display sub-components in separate images since they are separate things. If I used the same embedded data flow ten times, it will show up in the documentation ten times, which really I don't see why you'd want it there more than once. I get wanting to see all the logic for a flow at the same time, but if you've designed something to be modular, you probably did it for a reason. When I document code I don't repeat a function definition every time I call it.
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