So, I have the new board working by having the input lines jumper in a "pull down" mode.  The probe test has a resistor going from +5 to the input line. When this line is grounded, the circuit is active pulled down and triggers an action.

Remember I can't see your wiring so you need to be clear in what you say. Step by step...

So, I have the new board working by having the input lines jumper in a "pull down" mode.

This means you have configured the board to select an on-board resistor between the input pin and GROUND. That's what pull-down means - pull the input down to GROUND with a resistor. Now...

The probe test has a resistor going from +5 to the input line.

I don't know what you mean by "probe test" but if you mean the input pin again and you have a resistor between it and 5V then you're pulling the input UP (correctly) as well as DOWN (incorrectly). This is wrong. It may still work depending on the relative values of the resistors but you're making your system un-stable.

When this line is grounded, the circuit is active pulled down and triggers an action.

If by "line" you again mean the input pin, then this is the correct way to do it. HOWEVER - you should NOT have pull-DOWNs selected.