This is for a Mod, right? But presumably not yours?
Because if it's someone else's, then maybe they've tied the Jungle-clearance Worker-job to a tech you don't have yet? e.g. the Worldwide Mod doesn't allow it until way late in the game (and my W-i-P allows it with Engineering). But if you've already been able to clear Jungle on your territory, then maybe it's just banned within other Civs' borders, if you don't have an RoP (which presumably you don't, if you're at war with them...)?
Wasn't there a patch made at some point that made it an act of war for the human player to send his/her Workers into the AI's territory to 'improve' it, e.g. by changing their irrigation to forests?