I have the exact same problem with one of my apps.
The webapp directory structure gets deleted, but the war file is never unpacked. I have to manually unpack the war file,
tomcat restarts don't do the trick.
I have found various postings around the internet about this and I have found that the common denominators in my case seem to be when the application is a
struts based application and is deployed on tomcat 5.5.
Thus, I feel it is a tomcat 5.5 bug or a struts bug. But I can't figure out any more than this...