I've been patient with this Conqueror Ekko Bug...
This has been reported since Conqueror was introduced. It's time to make this rune work properly.
Ekko's passive doesn't give any stack for Conqueror. For instance, I auto a champion and Q them. The Q provides the remaining 2 stacks for Ekko passive and triggers his 3rd proc. damage. Conqueror remains at the same stacks even though this is a separate damage source.