I originally developed the fpga firmware and hal driver for pluto-p, but
I no longer develop them.  I don't even have a PC capable of running
the development environment for the FPGA anymore.

I do not recommend pluto-p for new users to purchase.  The Mesa
Electronics and Pico Systems FPGA cards are both superior in
functionality and reliability.

The specific problem you're experiencing is probably an incompatiblity
between the EPP protocol implementation in pluto-p and your PC.  One of
the problems with the pluto-p firmware has been generally-poor
compatibility with different EPP chipsets on the PC side.  When
performing multiple EPP reads or writes the PC and the Pluto end up
disagreeing about what register is being accessed, which (among other
things) ends up giving the wrong value for encoder counts or stepgen
feedback position.  Sometimes running with a shorter cable or with the
pluto directly attached to the parallel port will alleviate these
problems.

This is one example of the superiority of the Mesa and Pico EPP
products--they are designed with appropriate termination on the EPP bus,
while the Pluto is not.  This means that certain problems on the Pluto
board may be due to the board design and simply not fixable in software.

Jeff

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