Ken,
Since WARs are deployable units, and deploying source with your binary application is not considered a good practice, MyEclipse’s default treatment of the WAR won’t do that for you. (If you are just trying to create a backup-able or transferable copy of your project, File > Export > Archive is a better way to do that). I think we may extend that functionality in the future though (export WAR) to allow the inclusion of source for folks that want it. We can’t just sit on our high horse while users are asking for features 😉
Also the validator issue sounds like an install problem. The quickest way to trouble shoot this is to download our All-In-One installer, create a new install somewhere then open your existing workspace with it. Then right away do the export and see if it’s still running the validators. If it’s not, then it’s an install issue. If it is, then this could either be a bug, or a problem with your workspace. The trick here is finding out which piece of the puzzle is at fault, then tackling it.
If you get a chance (hopefully you are on Thanksgiving break?) to install the All-In-One, please let me know how it goes.