Firstly, thanks for taking on this mammoth challenge: brilliant job!
Using v5.0591 on Win7 machine. Alt is level 88, currently working in and around Pandaria Halfhill area. Almost every quest I get produces "this objective is not in the database" message when trying to use quest tracking in Carbonite. When I access the core WoW quest logging..the map changes and masks / hides the quest as soon as I move the cursor over it, so I can never query a quest from the map, whether it is tracked or not. If I disable Carbonite - this issue vanishes and it works as designed..but obviously, I prefer the far superior Carbonite system.
Also...I can no longer see inns or mailboxes whilst in Pandaria.
All the above issues just disappear as soon as the Alt goes to (say) Stormwind.
I know the Panadarian quests are not all manually entered yet..but I am not sure if the above is of any use or help, and/or whether I am the only one with these issues.