Had the same issue when I applied for the FAA in 99. Failed Ishihara plates miserably. I was then given a pair of Red Skiing Goggles and told to sit in the Cranwell sun for 10 minutes.
Went back in to do the Martin Lantern test and passed 100%. I was deemed then and there fit to fly. I also hold a CAA Class 1 as i'm an Air Traffic Controller with NATS so I guess it qualifies across the board.
Hope this helps, V801