Timer as a counter problem

Im using a PIC18F2220 to read two optical encoders.The job of them is to sense the speed of a DC motor and regulate it. I conected two opto interrupters to the Timer 0 and Timer 1,3 clock pins of the PIC. The one on Timer 0 works like a charm, while the other one only counts very shot pulses and ignores long pulses. (used Timer1 and Timer3 on it and bouth worked the same)

Can anyone explain why the other timer would behave this way?