This definetly sounds a bit odd.
Could it be something else on the computer reverting the .xml to a previous version after a reboot?
To find out, before starting Mach, make a note of the last change date/time (right click, Properties, and last change date/time should be on the first tab).
Then do what you have to get mach working, and check the last change date/time to ensure it's been updated (stupid question, but you are selecting 'Save Settings..' after you make any changes?).
Finally reboot the computer, and see if the last change date/time is still the same as the working version, or if it's reverted to an earlier date/time.