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Acording to Quartus this design can work with up to 16MHz, the crystal is 8MHz no PLL used.
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Did you specify a timing constraint of 8MHz, and the tool result was 16MHz, or was this just 'what you got'?
16MHz is pretty low. What speed grade are the FPGAs? I use FLEX10KA devices (older generation) and they work fine at 33MHz. It could be that your design style is the source of your problem.
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Part of the design is communication with other boards, I cannot reduce clock freq so easily.
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No problem, it was just a debugging suggestion.
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The design measures errors in step motor position and speed.
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I recently had to 'fix' a design that was a motor control interface. The original designers did not adequately decouple the FPGA, and there was lots of signal glitching on sensor lines when motors started and stopped. I had to add 'glitch' filters on the sensors, where the filter only allowed a signal transition if the input signal changed state and stayed in that state for 16us. The filtered signal was then sent to the control FSM internal to the FPGA.
What kinds of problem are you seeing on the boards that do not work?
Cheers,
Dave