I've got a 2001 cr 125 and started having rear brake problems. I still have a bit of brake pressure when i first hit the pedal, but the pressure seems to back off and the pedal will just keep going down. I was told it could be the seals in my master cylinder, so i completely rebuilt it but I am still having the same problems.
If you rebuilt the MC correctly and still have problems, either a leak at a banjo fitting or more than likely the rear line is ballooning. Time for a new rear line.