Update 2.0.13, the combining of the !QuestieCompatibility and Questie to !Questie breaks compatibility with some plugins. I think it's breaks the compatibility with Extended Quest Log.
After updating, Questie forgets which quests I have done and shows all as undone. Also it will track all quests in the game window, and quests can't be tracked/untracked anymore by shift+clicking them in the quest log. 2.0.12 works fine.

My plugins list:
Extended Quest Log (EQL3)
Cartographer
CEnemyCastBar
EquipCompare
OneBag
OneBank
OneView
OneRing
TNE_LowHealthWarning
WHDB

Link to my addons for testing: http://kug.us.to/files/WoW_Vanilla_1.12.1_Addons.rar

Thanks ill take a look into it, didn't have a chance to test it with other mods. I personally wanted to keep them separate anyway but multiple people had broken installs when they forgot to copy QuestieCompatibility

The problem anzz1 has faced with forgotten quests is due to neglecting to rename the Questie.lua to !Questie.lua in the character SavedVariables folder, and to a lesser extent rename the Account SavedVariables !QuestieCompatibility.lua file to !Questie.lua (and deleting the !QuestieCompatibility.lua file).

He is on point about the tracker. I can't comment on the incompatibilities, I only noticed an odd behaviour with FishingBuddy, which I disabled and Questie worked fine (albeit without the tracker working well).