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That's actually the way it's suppose to work, because carbonite's watch is a full replacement to blizzards rather then an addon that works with it, it sets whatever quest "autotrack" or clicking a ball to track as watched in blizzards just to enable the minimap blob of your current quest, and clears the rest.
However carbonite's watchlist should not be "disappearing" every login unless you have it turned off in the options.
The next release will have an option to enable or disable controlling blizzards watch for the blobs.
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