First, if you are using a GPS based system in a river, you will always have to adjust the speed setting to account for the moving water. For instance if you want to wakeboard at 22 in a river flowing 3 mph, you'd have to set PerfectPass to 19 when heading upriver and 25 when traveling downriver. It's doable but kind of a pain.
Second, try playing with your settings before going to the cost of an upgrade. I had exactly that same problem with mine - speed would surge and or drop when hitting rollers. I played with the KDW , Nn, and CS settings based on info from folks on this board and haven't had problems since (I'd tell you what settings I used, but I can't remember them).