Hi Babar,
I think you should first locate that which of the stg-2 board i/o lines are causing this problem.
Take the following steps:
1- Disconnect all i/o (encoders, d/a, a/d and any of the 32bits i/o) lines from the stg-2.
2-Connect the used bits 32 bits i/o to the required logic level by short links on the connectors.
3-Run the emc.
4-Connect one of the encoder with the stg-2 and move the associated motor manually or by
a 12V car battery. Check all the encoder same way and check for any noise on the counters.
5-Connect d/a output one by one and check the counters again.
6-Connect the used bits of i/o one by one and check the counters again.
I hope this will indicate the actual source of problem. This could be due to a faulty component
or inter connecting wires.
Nasir