spindle encoder cw ccw

Hi, I have cnc machine work with linuxcnc with encoder 360ppr every thing work will with max speed 600rpm in cw turn when i turn spindle ccw 
encoder stop counting and the machine won't move 

is there any settings to make encoder work in cw and ccw 

thanks for help

Can you look at the encoder channels with halscope? It is possible that the two phases are not in proper quadrature.