Got back to working on this one again yesterday.
After looking at the schematics long enough I decided to replace some decoupling capacitors in the timebase. The ones that seemed to make the most sense were C540, C541.
No luck, they were good enough nothing better after.
Then replaced C517 and C530, C530 was totally gone, nothing left to measure (over 40M
resistance and no capacitance), still no effect on my blanking problem.
Nothing related but I also stumbled across C750 in the final stage of the X amp that had never even been fitted.
My problem turned out to be T501 (BF199) in the blanking section. The transistor had more or less evaporated, all the AVR tester can make of it is a 30pF cap between B-E.
Happy end, thanks for all your input.