John,
The ordering of the buildpath is affected by the Order and Export tab, as you’ve already noticed. Naturally, it’s not great to have different versions of the same class on the build path but which one gets picked up should be determined by the first found on the build path, based on the order. Once you change the order to the one you’d like, I’d recommend forcing a rebuild of the project by selecting Project > Clean… just to make sure a full build is performed after the update.