A good place to debug would be org.jboss.ide.eclipse.as.core.server.internal.DeployableServerBehavior in the method:
protected void publishModule(int kind, int deltaKind, IModule[] module, IProgressMonitor monitor) throws CoreException {
It's possible this is an error upstream, but I really have no idea as I have not replicated it. But it seems strange for me. Even on an incremental publish, if 1000+ files were modified, it would be copying htose 1000 files.