Here's a little better example of what's going on. Traffic is coming through a reverse proxy on port 443. It is being forwarded on to a load balancer using port 443. The load balancer is doing SSL offloading so it is forwarding unencrypted traffic on to the Web Adaptor now at port 80 (It was 6080, but now 80). The WebAdaptor then forwards traffic to the ArcServer on 6080.
Browser <= 443 => Rev Proxy <= 443 => F5 <= 80 => Web Adaptor <= 6080 => ArcServer
I tried setting the WebContextUrl in the admin to httpS://gisserver.xyz.com/arcgis . It didn't seem to change anything. I'm not sure if it is the X-Forwarded Host Headers either, b/c the url's that it is returning have always been the correct url, just http and wrong ports (http://gisserver.xyz.com/arcgis) instead of http://servername.xyz.com/arcgis. I haven't checked the IIS logs, but shouldn't I be able to find those headers in the log?
Again, it seems like most urls are relative and start with "/arcgis/....". It's just the admin/login piece that returns the full url path "http://gisserver.xyz.com/arcgis/....". Not sure why it even needs to return the full url.