I reported this a while ago already. The pattern is completely consistent: if a quest exists in two versions – a low-level one and an epic or legendary one – then the epic/legendary version never gives any guild renown, while the low-level version has a chance for guild renown. Quests that exist only as an epic or legendary version, on the other hand, can give guild renown just fine.
So it clearly depends on whether the quest has a window where you can choose between a heroic and a legendary version: in that case, the quest giver can give guild renown when you do the heroic version with a character in a certain level range – while if you select the epic/legendary version, you never get guild renown. My earlier report unfortunately didn't change anything.
My suspicion is that these quests only grant guild renown within a single narrow level range, and that this check was set up for the heroic version. When you run the epic/legendary version, your character is always far above that range, so the check never triggers – and you get no renown. That would explain why it happens consistently and only with quests that have both versions.