A clone takes basic info from the configuration file, but it doesn't copy it, it generates a new one. This is because the mac information for the NIC must be unique. You didn't say what guest OS you are using, but you should be doing this from the guest OS NOT the configuration file, especially since the changes are not persistent. If you have to rebuild your guest OS for some reason, you are going to have one looooong day making all the resolutions back the way they were.
The guest OS should be able to modify it's own resolution and make the changes once it's running, and then clone it. The clone will then be correct.