1: Pretty much, yes. I used the VESA card I was experiencing almost immediate lock-ups with on the AOpen along with the VLB I/O card that I had been using on the AOpen. Waveform for bus clock on the SiS was absolutely rock solid on the scope. The AOpen one is quite noisy. Probe sat in there while Doom ran the usual demo3 without issues.
Also note that I have noise in some of the surrounding pins as well.
2: I replaced the RTC crystal at the edge of the board along with most of the other components in that area. Corrosion didn't reach the 14MHz crystal - and it is functioning properly (as shown in previous post).
3: I walked several of the ISA slots near the bottom of the board and saw the same measurements. To change things up, I relocated the I/O and VGA cards to the bottom ISA slots and probed the top ones. Same story.
I'll run the bench/test power supply that I've been using for the AOpen testing on the Soyo system and make sure the readings don't mimic the AOpen. If they are solid, then the PSU isn't at fault.
My money (possibly literally) is on the trace paths to the terminating resistor banks and/or the filter caps on the motherboard. It is also worth noting that there are several other places for capacitors that weren't populated on this board (various power rails for example) - It is possible there were more caps on the original version or only in design and they were omitted for this version's release as a cost-cutting measure. As a matter of fact, they are present in the front cover photo of the manual.