I made a little mod for myself which added new dialogue to two NPC that allowed me to buy some horses for followers. This was made under 1.8 and worked. However, with the new patch it doesn't work any more: the dialogue doesn't show up.

Before I go and drive myself bonkers trying to figure out what's wrong: does anyone know if patch 1.9 changed something regarding custom dialogue and or quests?

1.9 did not change anything in this regard. A few things to check:

1. Is your quest start-game enabled? If so, do you have a SEQ file for it?
2. Are all your aliases filling?
3. Are the conditions on your dialogue correct? (I assume so since it previously worked)