I think it has to do with the fact, that your new pes3 is patched. On your old ML there is also information about the kits. Now they are all mixed up with other kits. The ps2 reconize it as corrupted data. Same for the Players the ML. Maybe in your old ML file you have changed some players, and these are now all other players, with different stats etc. Maybe the PS2 also reconise that as corrupted data. That are the only problems I can think of. And mine conclusion is that you cant use your ML data again.. But Im not an expert at this.
Cheers
Cheers