so I checked through a load of different components; the CPU, the voltage regulator, the CPU clock, the DC input pins. Everything, if it displays a wave, displays that same square wave. I soldered a short lead to a ground point so that I could clip the ground connection in and free up a hand to measure the pins on the CPU more easily. I was hoping to see something different on the audio outputs.
could I be looking at a ground loop? all the voltage measurements I took look to be good, all across the board, it's just this weird frequency propagating through the board somehow.
Oh, and just to make sure it wasn't the oscilloscope, I did a quick check on my bench PSU and got a different signal