That's not a bug, when you upgrade all default files will be overwritten. Best is to keep a copy of keymap.xml, and replace it after an update. You can do the same with MediaPortal.xml (which stores ALL your MP Config settings) and all other plugin .xml files in your Program Data folder.
So I did not expected this behaviour and reported it as a bug.
For me this is part of the biggest annoyance of MP: Each update requires some amount of tinkering. I also have problems with the TV codecs and RarFileSource plugin since 1.3.0RC (but this is a different subject).
Positive note: The automation of updates is definitely getting better. I really like the new skin (Titan). And I absolutely love MP!
** EDIT **
Had another look and somehow the keymap.xml isn't part of the backup process (and the eHome Transceiver List + Wikipedia.xml neither). Think those files (or at least the keymap.xml) should be included in the backup process.