I had the same problem once. The printer did not want a raster file where all the colors were on one layer but seperated into three. It equated to a 3 color image, that way they could set their printers with one plate for each color.

I ended up using another printer who scaned the logo into their own equipment and I was out of the loop. The results looked great. Is your printer using Mac equip? The original printer did (I think most do).