Although I have no experience with these Rapido Rail Crew Uncouplers, I do have some experience with using magnets for uncoupling. I'm guessing that the RRCU's either have under-sized magnets, or under-powered magnets, or a combination of both.
Rare-earth magnets have a much stronger magnetic field than a same-sized ceramic magnet would have. However, the further away a piece of ferrous metal is held from either type of magnet, the less "pull" the magnet's field will exert on it. By varying the size and type of magnet, you can fine-tune it into the desired pull it will have on a piece of ferrous metal.
With that in mind, the size and type of the magnets used in the RRCU's are having less affect on the coupler trip pins, due to the small amount of added distance that the thickness of the ties and molded-in plastic roadbed of the Unitrack is adding to the magnetic field. If the RRCU's can't be opened up and larger and/or stronger magnets installed, then you'll probably have to resort to cutting the Unitrack's plastic base in order to get the RRCU's installed up as close as possible under the rails in order to minimize the distance between the RRCU's internal magnets and the coupler trip pins.
Hope this helps explain the situation a little bit.