Are you expecting the channels you programmed to be in pixelnet universe #1 or some other universe (like 2,3,4) ?
I recall always having to program it with jumper on universe#1 and then you have to remember to change to 2,3,4 afterwards if u#1 is not what you want.
Also, if you have continued problems, you might want to try the Falcon firmware (flashed on all 4 pic(s)) for ssc v4 and the usc ssc programmer instead.
Scott