LS6FD3S

My Brand new LS6 crate motor is throwing a Cam Sensor code at start up. It will not throw it when driving, it only throws the code only after usually the second start up. Sometimes it will throw a knock sensor code in the process. I checked the connection at the sensor which has a brand new oem harness by the way and the connection is good. I also checked the connections at the PCM and the pins are in the correct locations. Any ideas on what I can do to fix this problem? This is the only thing from keeping me finishing my swap. Thanks everone for any suggestions you can give.