GFP positive cells

I have been helping an investigator here with her studies of cells  
transfected with GFP expressing plasmids. The brightness of the GFP  
in many cases was such that the brightest cells were piled on the  
axis in FL1. However FL-1 was not compensated fully out of FL-2 and  
with that detector the negatives and and all positive cells are  
within the scale. However there are some cells that show up positive  
in FL1 but not FL2. The data looks much better in FL-2 but we are not  
sure if that is valid. Any thoughts as to why there would be many  
cells that were less orange than would otherwise be expected? Perhaps  
slight alterations from cultured cells ingesting GFP from other  
cells? Attached is a figure of this.

William Schott
Flow Cytometrist
The Jackson Laboratory
600 Main St.
Bar Harbor, ME 04609
Phone: (207) 288-6192