You're over-thinking why they suggest using the internal ignitor with the v3.0... the simple reason is that the v3.0 board was equipped with one whereas the v2.2 board was not.
In other areas of the manual, specifically where multiple outputs are required to trigger a multi-channel ignition box, internal ignitors are forgone in favor of the same configuration the v2.2 board would use for a single channel.
The v3.0 board is really designed rather well, so I still suspect the problem may lay within the circuit configuration and not the physical layout. The only differences between the v2.2 and v3.0 boards that I see are the LED driver transistors. The v2.2 board uses 2N2222A transistors, which have a higher collector current rating than the v3.0 board's 2N3904 transistors. Either way, this difference shouldn't cause a problem.
If you've run a jumper directly from the cathode of D17 to the DB37 connector, I recommend adding a 1k ohm pullup resistor if you haven't already. If that doesn't work, try adding a 330 ohm resistor inline between the LED and DB37 connector to limit current and thwart any possible loading affects.
