I had that exact combo working on a 486 back in the day. I had that card and a 250MB Conner as my older of 2 drives (I think it was connected as primary slave). I don't know if it was the same model drive but very likely so. Back maybe 15 years ago I could have been more helpful but I don't seem to have the drive anymore and I don't have a VLB motherboard anymore either.
I might still have the manual, but if that website was a copy of the manual then that won't do any good. If there's any doubt about the website info then I can look for the manual though.
I remember my 40MB Conner needed some revised/undocumented jumper settings in some cases even with older cards, and I never got it to work at all with this EIDE VLB card. But I don't remember having any such problems with the 250MB.
Back in the 90s my first VLB IDE card (a different, unknown generic card) was defective and had symptoms like this. It would fail to detect the hard drive 9 times out of 10, but then occasionally would detect it and boot normally. I never found a solution other than returning it. I also had the same symptoms on an IBM laptop when a service shop swapped the motherboard with one that apparently had this same defect - again it would boot successfully about 10% of the time but otherwise kept producing this detection error. Again, it was only fixed by having the board replaced.
So I have to say that I've seen this symptom on defective IDE controllers twice before, and from what I've read on this site, VLB cards in general are apparently known for being flaky in old age. My Acculogic sIDE-4/VL card was always totally reliable but that was back in the 90s.
Hopefully it's just a jumper issue but I wouldn't be surprised if the card is at fault, maybe a cracked solder joint somewhere or dirty contacts.
Have you tried different slots or poked around in the motherboard settings? Since the IDE function might be the only part of the card that cares about VLB, I wonder if it's possible that dirty contacts in the extended part of the slot or some kind of configuration problem between the card and motherboard could cause issues with IDE while everything else works normally. I'm just grasping at straws when I say that though.