I used the LSI7266 counter chip (2 channels) for encoder input and 2 X Allegro A3959 motor drivers.Just to clarify, did you use a quad decoder or quad counter, such as the LS7166?
The application was a piece of cinema gear requiring precision motion control.
There are two main software modules required:
1) PID position servo loops
2) Trajectory generators (indexers)
It's a massive project to get all this stuff to work correctly, this project took MONTHS to finish, a gnarly beast.