I use the same bottle filler. The whole idea behind a counter pressure filler is to have the keg and bottle at the same pressure...then when you slowly release pressure via the valve on the filler, the beer will start to flow to the area with lower pressure (bottle). In your situation, it sounds like the keg is primed, so we're not really sure the pressure on the keg. You also need to make sure that the bottle is pressurized before switching the ball valve to the beer side. You want to pressurize the bottle, vent co2 to purge, and then switch to the beer side. I've hit the bottle with the beer side before pressurizing and it's all foam.
I think your issue might be related to a pressure difference between the keg and the psi you are using on the gas part of the bottle filler. I force carbonate, so I have the kegs hooked up to 12psi and the filler hooked up to 12psi. When they are equal and the pressure valve closed, no beer should flow. If the gas side pressure on the filler is higher than the keg and you pressurize the bottle and switch to beer, the beer should almost reverse back to the keg. You want the pressures to be as equal as possible so that you can regulate the bottle's pressure a little lower so that beer will start to flow into the bottle.
I use 12psi on 5ft beer line, using cold, wet bottles and get almost no foam.
Let me know if you have any other questions.