I am having the same problem. I have my corporate site in (My)Eclipse. When I deploy (as an exploded project to Tomcat 5), it updates _every_ file, including year-old, large PDFs and images. It takes a long time, longer and longer as I get more and more of the site imported.
I have Eclipse 3.0.1 on a Windows XP machine with MyEclipse 3.8.4+QF2. I read the documentation and didn’t see the question answered. (Did I miss anything?)
Thanks,
Dennis