Whatever your new board is, it may invert the input signals.
There are many combinations of inputs, all configurable on Mach 3 - you say you are using Mach 2, but this will probably be the same.
The thing Mach needs to know it what signal it will see on the pin when the switch is activated.
Switch on your machine and, without anything running, manually activate the limit/home switches. If you look on the diagnostics page, you should see these switching - if they are active.
On Config/Ports and Pins/Input Signals then ensure that the limit switches you are using are enabled (Column 1), and all are correctly designated to Port 1 pin whatever you are using. Then go through each one and make sure that when you switch the switch, the appropriate led lights up. If they are already lit and they go out, then "Active Low" for that pin needs reversing.
If you get no signal at all then there is a interface problem with your new board. For this you will have to test the signal coming from the switch to your Bob board, voltmeter will do, and ensure it changes when the switch is pushed. If it does - but this is not getting to the computer - then a bit of headscratching is called for.
I think thats enough for now