This will be my last reply until Will replies tomorrow.
When you have no ground at all, you will often see ghost signals on a scope -- signals that aren't actually present at the point you're touching with the tip of the probe, but in fact are picked up from elsewhere. (60Hz, for example, is common for a ghost signal to appear on a scope display.) A probe GND-lead properly connected to the correct ground will kill the ghost signals in most cases, unless the ground lead from the scope probe is very long (e.g., like your green ground lead), in which case that long ground lead acts as an antenna that can detect ghost signals (which again, aren't actually present where the tip of your probe is touching).
When you have a very short ground lead, it effectively cancels out the ghost signals and can explain that one measurement on your scope where you thought you'd get a signal but didn't. I believe the short GND in that one measurement was doing its job.
I've never measured signals on either Y3 leg, and I suspect Will plans to do that tomorrow morning for you, which is good because we need a frame of reference from another tester for that. And maybe the conclusion of the Y3 testing will be something that can be added to Mac84's SE/30 document so other people in the future need only reference that info.
Also, I cannot see a clear photo of your scope probe to see what your attenuation slide-switch setting is. But if the on-screen message below means your Probe is set to 1x, that needs to be changed to 10x for correct HF measurements. The 1X setting can be used for very LF measurements, but it's best to only use 1X for very small amplitude signals that are hard to measure with the 10X probe setting.