@BrettKuntz, If you are clearing all the ports on the Port Management page, then on any upgrade or update of the module we attempt to find new unused ports that we can use. This may take some time and may be the cause of your issues.
As for the issue when you change the apache port, we attempt to grab whatever you had before you submit the page, so if that’s not working, can you please open a bug at issues.freepbx.org so that we can take a look and get that addressed.