I had the same problem. When I set the pixelnet plugin to start at channel 513, all the SSCs were shifted by 512 channels. I changed the pixelnet plugin to start at 1 and everything worked fine.
If you set the pixelnet plugin to start at channel 513, the first SSC for channel 513 has to be programmed to channel 1. In other words, subtract the number of DMX channels from the channel number and program the SSC to that.
If you want the SSC set to 513, set the channels for the pixelnet plugin for 1 to 2560. Then, things should work as you expect them to without having to reprogram the SSCs.