Jporter,
My vortech controller does the same thing but everything works as supposed to. I verified that everything is working correctly by going into the program for each pump and turning the pump off for a maintenance cycle. For instance, I put pump one on maintenance 1 and pump two on maintenance two. The correct pump shut down when I turned on the maintenance cycle so all is good.
Just make sure you have 255 as 100%. I ran my vortech module for months before I realized I was only running at 30%. In order to calculate the % you want your pumps at its .?x255=Pump Percentage. For instance if I want my pump at 80% then it would be 0.80x255 = 204 in the controller.
Jared