Also I have found (by own stupidness) that you cannot put mc360 into the new builds of xbmc before putting xbmc onto xbox, mc360 needs to be put on after xbmc is installed, otherwise you will get problems. I used to think that overwrite was the answer....but like Blackbolt said
WIPE MC360 and reinstall it, never, NEVER overwrite.
The way I do my upgrades is to change to PM3 skin first, open FTP and delete my XBMC (complete directory), install my new XBMC (without mc360 skin), reboot Xbox, re-open FTP and send mc360 skin. Now I never have any troubles.