I get exactly the same problem. Sometimes new quests aren't displayed on the map and the tracker. If I look into the Blizzard-log (ALT-L) it is also not listed, but it's still active and I can complete it normally. Restarting the game etc. does not help. The only solution I found is to disable all AddOns. When they are disabled I get the quest listed in the official log the next time I log in. Then I can log out and enable the AddOns again. When I now log in the quest is still there (on the Carbonite-tracker, the minimap and the Blizzard-log) and everything works normal again, until I get a 'problematic' quest again. Later this day I will try if disabling Carbonite is enough or if I really have to disable all my AddOns (I haven't tried this before, 'cause clicking the "Disable all" button is easier then searching and disabling Carbonite manually, because I use a lot of AddOns ^^). I will report later then, after I got a problematic quest again.
Additional info: There were also a lot of quests missing on the tracker, map and Blizzard-log when I logged in the first time after the 3.3.2 patch was applied (they were normally shown just before the patch was live). From about 15 quest i had in the redridge mountains only 3 or 4 were shown and newly taken quest also doesn't show up, only after the logout-disableaddons-login-logout-enableaddons-login thing ^^
I hope this issue can easily be fixed, 'cause I really love Carbonite and don't want to miss it.
By the way, I use a german client, so this seems not to be a problem with the french client @ Aximili
P.S.: Any incorrect spellings, grammatical mistakes and similar things are only for your entertainment! I hope you enjoy them and don't blame my moderate english-skills. 