Well after some digging and comparing. I solved that part of my issues. I created a 1 inch cube stl file. I did a direct print in m3d( sort of I aborted the print) to get the file logged into it's que log. Basically a print log of the jobs and the gcode used for it. I then added the S3D gcode file via the advanced menu in m3d software. It bombed with the unknown gcode error. So I pulled that que logged file to see what it contained. I tried to do a direct comparison between the 2 que files to see if anything was obvious. Well the best I could tell is they have some differences. I am not a full fledge gcode coder so that makes it more of a challenge to a direct comparison. Needless to say I have been playing with it and looking around the web for info on what gcodes this uses. I have a small collection of 14 so far outside of the basics like absolute mode etc. While not extensive it does help me a small bit to see what they do, like heaters on etc.
When I was looking at the gcode from the S3D I kept seeing M101,102,103. Then it dawned on me that I saw that in the process menu, a check box for adding these codes. So out of curiosity I manual input them in the advanced menu in m3d, send command line to see what they did. Those are the codes that are unknown. So basically I had that check box on in S3d and the m3d does not recognize them as valid.