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The below might be correct, but I suspect not particularly helpful...
I've been doing a bit of reading up on autoconfig, and my understanding of the situation is thus:
Autoconfig is enabled for boards when they receive a signal on the config_in pin of the zorro connector, but rather than use a separate config line for each slot (which would limit the size of backplanes) the boards are daisy chained such that when one card is configured it passes the config signal to the next slot's config_in. There is some logic on the backplane to determine if a slot is empty and pass the config signal to the next slot.
So, I would guess that the autoconfig logic (or one of the PCB traces or associated components) of the cybervision is broken, in such a way that it is not only not configuring the card, but also not passing the config signal along, so as far as the Amiga can see, there are no autoconfig boards attached with the cybervision in the first slot. This doesn't offer a solution to your problem though.
It's also possible that the edge connector of the card is just dirty, it would not hurt to give it a clean to ensure that it's making good contact with the backplane slots.
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