The LPT port addresses, LPT1 and LPT2 are, in actual fact, three addresses each in the PC.
LPT1 is &H378, &H379 and &H37A, LPT2 is &H2278,279 and 27A
378 and 278 are the OUTPUTS for lines 2 - 9 on the 25 pin port (the old printer data pins). 379 and 279 bits 3 - 7 are the 5 input lines( pins 15,13,12,10 and 11 - note the order)(see later) and 37A and 27A, bits 0 - 3 are the other output pins, 1,14,16 and 17. Pins 18 to 25 on the port are signal return (0v) connections to the computer.
The LPT1 port was normally in built in the motherboard of the computer and therefore the input/output capabilities are fixed, whereas a second port if added as a plug in COULD have bi-directional capabilities, depending on the board.
If your LPT1 port is buit in, there is no point testing it - you cannot change it - but you seem to be saying that you can changes the input/output capabilities - so are you using two plug in ports, or is your first one fixed and the second one a plug in.
I have never seen the need to muck about with my computers BIOS. If your computer is working properly (and I like the touch screen, I have one on my organ simulator) then the basic operating system - to be compatible with the IBM PC format - should already have at least the LPT1 port properly addressed and formatted.
If the port is an add on, and you have the axis and spindle working, then it would seem to me that your port card is switchable, and you have the input pins designated as outputs, so although the card is seeing the inputs, in is not passing them to the computer.
I think that is all I can say at the moment till you have another "fiddle" with it.
In Mach 3 set your port one address at 378. If your switches are live, then go to the Mach 3 diagnostics screen and see what the led.s show for activity on the port. They light up if an active signal is detected so toggle the switches and see what happens.
If you use your port test program and that is telling you that the inputs are being detected when you switch them manually, and the led,s on Mach are not showing then your configuration file on Config/Ports and Pins/ Input Signals needs attention. The favorite thing on that page that I kept missing was the port number !!!