I seem to have discovered the issue.

My default rviz config (in ~/.rviz/display_config) has field which are
named the same way as the config file which I am loading. Their
enabled/disabled state seems to persist when loading a new .vcg file.

Example:

* display_config settings:

X enabled
Y enabled
Z disabled

* mycfg.vcg settings:

FOO enabled
BAR enabled
Z enabled

 * Start rviz, load mycfg.vcg, result:

FOO enabled
BAR enabled
Z disabled

Is this a bug, or am I misinterpreting the way that vcg configs are
supposed to behave?

Thanks,

Ivan