I am using Eclipse (Ganymede SR1) and Idea (8.0) on the same project. I setup Idea and Eclipse to use different output paths. For some reason Idea would not update the .class files under the exploded directory. After some head banging on the wall I figured out that I setup the output of Eclipse to be WEB-INF/classes directly under the web root. I compiled the classes under Eclipse and then switched to Idea. Idea would properly compile the classes under exploded and then copy the files from the web root, overwriting its files with the old Eclipse generated .classes.
The temporary fix is to delete the obsolete files under the web root/WEB-INF/classes.