Custom setting e3 does not matter if the SB-600 in in the hot shoe. E-3 only effects the operation of the built-in flash.
The Nikon support rep must have misunderstood you or had his "cheat sheet" open to the wrong page. I recommend that you always ask questions here on Nikonians before trying Nikon support. You are more likely to the best possible answers from members here with a lot of hands on experience. This Nikon support reps cannot possibly have firsthand experience with every camera that they field questions about.
Remember, Nikoians are always here to help!
Dave Summers Lowden, Iowa Nikonians Photo Contest Director
Nikonians membership - "My most important photographic investment, after the camera"