This isn't a ccmerged issue. The skill gain is determined by the script itself, which does not rely on the ccmerged.package. There is something else causing the sim to not be able to gain the skill. Have you tried using the Tree of Prosperity with a different sim?
Ricalynn's suggestion is the best and it's what I would have suggested. If installing Lunar Lakes/Tree of Prosperity into a clean folder makes the Tree of Prosperity work, then there is something wrong with your current Sims 3 folder.
You could also try resetting your sim with the resetsim cheat. It is possible for a sim to get corrupted and not be able to gain any skill, although in that case I would expect the sim to reset when trying to use the fruit. It's still worth a try.