I use the tweak setting to change the apache port (to run behind varnish), and we often use subdomains. This used to work fine, but for the last week at least (hard to tell b/c we don't create them every day), the virtual hosts created by whm all use the standard port, disregarding the tweak settings.
Currently running WHM 11.40.0 (build 9)
Currently running WHM 11.40.0 (build 9)