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Hi. I wrote the patch that was applied in the most recent version, and I think I have seen your issue too. However, I don't understand how my patch could have fixed it.
It is related to config copying. If you load a config and then immediately try to save it creates a direct copy of the config you just loaded by parsing it and saving it out again, without reading or writing to the xfconf. It seems like because of this it is possible that you can make changes to the config while panel-config is still running and they won't be saved.
The patches I sent were to prevent some crashes if the config is corrupted externally.
Because we are really close to release I did not try to fix this issue with config copying, as it would involve getting really deep into the code. You should be able to work around it by restarting panel-switch after loading and before saving, or by using the command line interface eg:
xfpanel-switch save path/to/
xfpanel-switch load path/to/
The command line interface does not do any fancy config copying at all. It always saves/loads immediately from/to xfconf. So it should not have this problem.