I haven't spent much time with the VP-100, but here are a few things to try. First of all, set the up and down positions a little shy if their actual position locations on the sensor. For example, if 0 is all the way up and 255 is all the way down, set them at 10-15 and maybe 240 and set them to run 2-3 seconds past the position. Make sure you don't turn power on with the flap switch locked up. Running 20 seconds past the up stop is a problem. IIRC, the flaps are set to disable if they run for 15 seconds non-stop. It could be that it isn't quite reaching the up position on the sensor and keeps running until it disables it due to thinking it has runaway flaps.
Let me know if any if these things help.