Bizarre - that's almost exactly what mine did. Twice! After ftp-ing my backup copy up it worked for a while and failed again. Same problem - file has lots of junk in it as well as the real config.ini. So I parked a copy of config.ini in /drive0 so I could do all this faster, reinstated it and fscked while watching an interesting program about the Falklands (well interesting to me) and have had no problems since.
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Rory
MkIIa, blue lit buttons, memory upgrade, 1Tb in Subaru Forester STi
MkII, 240Gb in Mark Lord dock
MkII, 80Gb SSD in dock