SP favor works correctly...
MP, especially Pantheon does not... Supposedly and I could be wrong, that when searching for a game on Pantheon if you cancel the search for any reason(someone not connecting, connection hanging because this, etc) it subtracts favor. I'm not 100% on this but it sorta seems correct. Also again not 100% supposedly if you bought a favor item pre-release(people who got game at GS) the item amount was subtracted at start of the release Tourney(again not 100%) but my favor was in the negative for the exact amount of the one favor item I had at start of release.
As the Pantheon favor was working correctly, from Friday to Monday when I played it, although I am not sure what has happened since Tuesday. But I'm sure as soon as they get the MP stuff sorted out this issue will be fixed, along with the rankings and game tracking which also seems messed up(i.e. losses for games that are dropped being counted as a custom game, or games not even being tracked, or losses just showing up even though you never actually played the game but were in a search that never went through.
