Rob,,
The fundamental reason for the problem is, as you have rightly guessed there were residues. But what caused these residues?
If you are using GPE, the first time you run it, it would ask for webapp directory. Select target/<web-app-name> for that. Do not use src/main/webapp which is for a different purpose.
Do check if you still have GWT compiler output in src/main/webapp, if yes, you are likely to run into the same problem again!
Hope this helps,,