I know this has been posted before but I've tried everything to get them to show in Carbonite. I don't remember what version I last saw them working.
Version:
-Carbonite.toc shows: 5.2.1 alpha 9r2
-Carbonite message when first logging in shows: Carbonite 5.1.6 B292 loading
-Top level of Carbonite Options shows: Release Version: 5.1.6
I completely exited WoW.
I've deleted all Carbonite* files under the folder:
...\WTF\Account\<accountname>\SavedVariables
I've disabled all addons except Carbonite and Carbonite Quests (Even left rest of the Carbonite suite disabled).
When I logged back in I could see quest blobs on the mini map, but not the Carbonite map. I said yes to merging the 2, it reloaded - still not showing on Carb map, only the docked mini map.
I made sure the Green button on the quest tracker was enabled (I see the circled X on the map where the quests location center is, just not the blue blob showing the quest boundaries)
I made sure right-click->Show->Quest blobs was checked.
One thing I did notice is I was in Kun-Lai when testing this and in Shado-Pan Fallback (tower that leads to the top of the wall). The Carb map shows me there but when zoomed out it also sometimes showed me between Pandaria and The Maelstrom/Kazan/Lost Isles maps, right in the black area with 2 exclamation points one saying Inkkill Mere, the other was Nayeli Lagoon. If mouse was over Pandaria it showed me in the right spot, if it was on any other map/continent it showed me in that black void.