OK, sorry for the confusion! Yes it's really hard to explain this..
So, the panels that I am running consist of 9 individual PCBs. There are fids on the panels, and on the PCBs. From CAD, I exported the centroid data on the entire panel itself. So in essence, the pick and place treats the ENTIRE panel as a single board. I did this because it is so easy to export out the data on one file, and I don't have overly fine pitch components, so I don't need the PCB fids. But if I ever need, I can use the PCB fids and just set them as a local fiducial.
Every ODD PANEL gets missplaced (0, 1, 3), while every even panel is fine. I'm sorry, but I don't see how it is possible that the conveyor or anything is the problem. The machine finds the fiducials every time, so even if the panel wasn't on the rails properly, the fiducials would either error, or they would still be found, and it would correct for it. Also, it wouldn't be every odd board, it would be random.