Aaaahhhhhhh last night left me feeling so horrible...
I opened up my oscilloscope and I opened up the AT board enclosure. I found the error almost at once. An obviously broken solder to the BNC connector well that was a simple fix I thought! I resoldered it and reassembled and... whole scope was acting erractic and weird, I even lost the traces sometimes. Lost the ability to modulate the amplitude (v/div). Was feeling really down, thinking I broke the scope with ESD, I had it on a mat though and I kept touching an earthed metal piece now and then. I was pretty sure I'd gone and ruined something. Went to bed feeling pretty lousy.
Fortunately I got a tip from someone else and I started looking at the ribbon cables. Turns out one of them had broken but looked whole. I soldered in another cable for test and hey it works again! Now I am feeling really satisfied
Both channels work identically now, feeding a 3khz sinewave from my computers headphone socket:
I still need to properly replace that 3-ribbon cable however.