Pulse counting affected by oscilloscope probe
Here, probably the optocouplers does not transmit 128Khz signal with good quality (what is very easy with wrong designed schematic). So, the pulse counter (what is the input?) simply misses some of the pulses. 

In addition, when you connect the probe capacitance in the circuit, the quality of the signal becomes even worse and the counter misses more pulses.

Try to put Schmitt trigger on the other counter input and see what happens. Also revise the optocoupler part. Try to model it in order to check the frequency characteristics.

Adendum1: If you state that the signals are perfect (and if they really are), then your counter probably does not count properly. I can't see any other reason for such weird behavior. 

BTW, some time diagrams might greatly help the analysis.