I'm not sure if cleaning the project will get rid of them. Have you
tried that? I've added the WTP newsgroup to the "to" list of the reply,
since I think this function is coming from there.
This is a known problem, and should be corrected with Eclipse 3.4M7 and
Web Tools 3.0. You have the ability to select and exclude certain
files from validation with Web Tools 3.0. Also, the Platform has added
the ability to get rid of the extraneous error markers as well.