Is it a toroidal transformer or just a regular E-I type?
I've seen videos of bad toroidal transformers in test gear.
But it is quite unusual that your scope probe would cause so much noise that it makes the measurement so misleading.
Anyways, i think the power supply instability could be causing a brown out or a latch up in your board.
It might be worth trying to power the board externally to isolate the power supply issue.
Does the transformer get hot/warm after some time running?
Also could you measure the unloaded output of the transformer when you poke it?
It's mounted on the PCB and E-I style.
IDK whats causing it but its pretty typical for me to get 100-200mv of noise when using the long grounding lead. It always goes away when I use the little spring ground wire.
I don't have a low impedance source of AC right now. so I can't fully power it externally, since it has a -8v rail too. but I squinted at the schematics and I think not supplying -8 is probably okay. If not okay I think only the analog output on the board would catch fire which is not important to me. <hold while i hook it up...> everything's okay applying 8.5v to the output pins of the bridge rectifier (and of course not attaching the transformer) about 270mA DC, very steady. I'll let it run for a couple hours and see whats what
Transformer gets warm. I'd say 35C, using my fingers.
Unloaded and cold it doesn't glitch that I've seen. I tried the resistor dummy load to see if the voltage was sagging because of transient loading and that doesn't seem to be the case, or at least not the only case two things can be broken at once or one cause fault in the other.