So you restaked the nut... was it in the same spot? Or a different spot? Or did you use a new nut?
I've always been told to use a new one every time, but if the old nut indexed differently the second time maybe that tells you something...
82 fj40, 99 uzj100, 06 gx470
97 DR650, 05 525EXC, 01 XT225, 09 TTR125, 07 TTR90, 07 CRF50