Brixia,
If you have a series of machines that has been getting no errors and then you end up with 2 machines that are showing the problem, I would tend to ask a couple of odd questions...
Such as-
1. Are the problematic machines built around the same time approximately?
2. Is there anything that is uniquely different between a machine built like the problematic ones and the other majority of machinery.
When you look at the machine for problems like this take into account the way that the interface cables are routed between the ACC-24V and the PMAC-VME. I think that you indicated that they have been replaced. Be sure that they are as short as possible...
If the problematic machines were built around the same time, could there be a unique wiring change that is causing a ground loop between the encoder processors and the ACC-24V.
Unit101 referred to checking the grounding between the encoders, 5V supply and the controller. Insure that the connections are present and that they are tight. If the machines are just a couple of units that have been operating in the field for a while, then vibration and galvanic corrosion can affect the ground bonding around the machine. A ground loop can make the ACC-24V and PMAC interface flaky...