I too am having similar problems with the Quadrature Encoder.
It seems to only increment the counter on the rising edge of Phase A, or every four clicks. This divides the effective resolution of my encoder by 4. For true Quadrature Encoder decoding, the counter should change on both the rising and falling edges of both Phase A and Phase B.
I would be interested in getting that aftermarket code for real Quadrature Encoder decoding from you. I assume you used interrupts for this?
It would be a good enhancement for the next firmware release of the PLC to fix the Quadrature Encoder decoding. Even on the falling edge of Phase B, the counter should change value. If Phase A is high, then it should decrease, if Phase A is low, then it should increase.