Derek,
In KMS, the .kms file is always correct. So if you have made hand modifications to the system.h file, those will be overridden by the values in the .kms file.
There is no way for the system.h file to be parsed and the values therein updated into the KMS GUI.
You can share .kms files between multiple computers. You need to keep the .elf file and the .kms file together, so that KMS knows the memory addresses of your variables.
The document: Adapting KMS for Custom Hardware goes through the preferred path to generate a system.h file for your custom hardware using the KMS GUI.
There isn't a log of what the GUI is doing behind the scenes. My guess as to why you are seeing that issue is because your system.h file is misaligned with your .kms file.