I have an odd issue. My A4000 has a Macrosystems Warp Engine with a 68060 mod on it, SCSI and 128 MB of RAM.
When I cold boot it in the morning, it will not see any Zorro cards at all - (I can tell because it has RTG Graphics). Showconfig will show the Macrosystems card, but not my Retina, AD516, XSurf 100 or V-Lab card. The interesting thing is if I leave it on for 5 or 10 minutes, and then reboot, all the cards show up, and the computer works great for the rest of the day! Even if I reboot, or power cycle it, ZORRO works just dandy.
I have a similar problem with an A4000 that has an unmodified 040 WarpEngine. My A4000 had been in storage for a few years and when I re-started it, none of the Zorro cards could be seen by the system; X-Surf with Subway on clockport, CyberVision64/3D. The Zorro problem in my case persists, and the cards never do show up after warm-up. I never did figure it out and eventually put the machine back in the closet. Maybe I'll have a look again and remove the WarpEngine and see if that is the culprit.