Most all Digitrax HO-scale decoders have the 9-pin connection, and have for as long as I can recall (going back to the DH120's at the very least...and that's around 1998, IIRC). Lenz and NCE I believe also use them on some decoders. On the Digitrax DH12x series, those two extra wires serve no purpose and I snip 'em. On the DH14x and DH16x types, it's the function leads for F1 and F2. The nice thing about 'em is that they are keyed, so it's not possible to plug them in backwards (unlike the NMRA 8-pin). Also, they appear to be a lot more robust in use. For example, I've never broken a wire off a 9-pin decoder harness, but I have broken several 8-pin connectors (either the wire or the pin has broken or fallen off). Personally, I prefer the 9-pin over the 8-pin for the above reasons. As for the manufacturers, I think it's also because the 9-pin connector doesn't need the room and circuit board space that the 8-pin requires.
Paul A. Cutler III
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