Sorry for the delay, heres what it looks like.
I left the default frames on as a workaround, if i click on the wow UI accept then it properly watches them. I am not sure if to get THAT to work i had to manually turn back on the cvars autoQuestProgress and autoQuestWatch to 1 (using another addon) which carbonite seems to disable and not turn back on even when deselecting the quest module option or removing the mod.
as you can see next, the quest is not watched even in the log
if I click on the wow blizzard ui frame instead then it is watched both in the tracker and the log.
Edit: I snooped around on the LUAs but was not able to find the cause to make your life easier. Storyline seems to fire the blizzard QuestAccept method and yours looks for the QuestAccepted event which should interact. I did see some section in your code with some custom hook for accepting quests but I dont know if that would cause the issue.
Part of the draw of using storyline besides the lore experience, is that you can select menu options and accept quests using the keyboard.
carbonite seems not to autowatch abandoned quests no matter what so its been difficult to troubleshoot