For anyone still interested in this, I keep having this problem but found a simpler workaround. If WTP/JBoss Tools fails to deploy WEB-INF/lib's content, just closing en re-opening the affected project and then executing a Clean on the JBoss Tools Runtime Server seems to solve the problem temporarily.
I also encountered another problem, quite like this.
From SVN I had some new incoming libraries. I performed a clean again in the hope that the deployer would pick up the new libs, but unfortunately it did not. I did deploy everything that was supposed to go in WEB-INF/lib and had been there before, but just not the new ones. I doubly checked that clean actually removed the old deployment and copied the jar files fresh to WEB-INF/lib. This indeed happened, but somehow, somewhere, WTP remembers which jars have been recently added to the project and it just skips those.
Luckily, closing and re-opening the project and doing the clean solved the problem.
I love Eclipse, I love WTP & JBoss Tools but at times it all can be a little maddening... ;)