There is currently a problem with the way WW is creating Proxy meshes. At this moment, you may have unexpected results with the Proxies if you click the Update Selected Proxy Meshes button in WW and the original WWMT mesh is offset from the world origin.
I'm working on a fix for this.
Unfortunately, this also interferes with another upcoming update to WW that allows loading/changing entity props on the fly by importing QCs, using a model library or loading from scene WWMT/Proxies. When this new version is updated, there will be a set of steps provided to fix any proxies in current scenes that are updated with the update selected proxy function after this upcoming update.