@Don,
Fair enough. I am probably in the minority here when it comes to cap replacement. It doesn't make for a good preventative maintenance practice IMO. Because you really don't know how long those caps will last. No one can say for sure when they will fail. Usually parts that you can predict when they will fail can get placed on a scheduled replacement basis (ex. car analogy - your tires, your brakes, etc). Otherwise you risk overmaintenance and wasting money. I guess I take that approach because I work in the repair business as an in-house engineer for a biotech company.
As for the XY vert mode, you say the anomaly disappears when the scope is in that mode, but in one of the photos you shared (when you make a straight line), I can still see the anomaly at the top of the line. Looks kind of like a hook. So I don't think its safe to say it disappears in XY mode.
The reason I asked about the pre-amp is because each channel has its own pre-amp. So it would be unlikely that you'd have the same fault in both channels (though not impossible). That's why I'd be looking further downstream of the pre-amps (vert switching, output vert amp). And it is definitely still worth looking at the CRT circuit.
Granted, this could be from a switch with a dirty contact or something as well. In my experience, 9/10 times this complex issues tend to be from something stupid like that. Still worth going through the schematics and following an injected signal thru the vert amps to see what you get.
-Frank
Frank Mashockie