something i found is that the connector between the bvision and ppc boards can "bend" slightly. this can happen if you over tighten the nuts and bolts - or seemingly over time with the force of the mounting kit, and lets face it, 1996 was a good amount of time ago. Resulting in giving you a good connection at either end of the connector, but the middle can be visibly seperated. if i ever put my bvision and bppc back together, i'd put a thin piece of something solid across the top and bottom of the cards as a load spreader that the nuts and bolts would then put pressure on - rather than the PCB material itself. spreading the clamping force across the connector evenly. i rememeber this would give me crashes and instability enough to drive a sane person to the brink.
i'd also make sure that all the big square chips on your bvision have heatsinks. there is what i guess a fat CPLD chip that's doing a lot of the PCI translation, this gets really hot too. if these chips are NOT getting warm, then we either have issues further down the pipe, or it's just not getting power.
i gave up with cybergraphics years ago, bascily when i could no longer put the original CD in as part of the install procedure. are you using cybergraphics or P96?
sorry to hear that you're having these issues, and i hope you resolve this soon. i would say please make sure that your powersupply is good - i used to run an extra 5volt line from the molex cable loom for drives to the 5volt of the floppy connector on the mainboard. hope i don't sound like i'm trying to tell you how to suck eggs!

good luck, please let us know how you get on if there is any resolution.