I have been having a very similar issue. We are also running vR9.4g.
We are using a pac-s controller. We have an identical computer running a much more complex but similar program that does not have these issues so IMO it can't be the specs of the PC, though I can provide the specs if need be
Some quantities are remote IO points, others are just float variables. I have checked the voltages to the racks, they are between 5-5.2vdc.