Think about it !!!!
The diagnostics page shows whether the COMPUTER thinks the switches are ACTIVE or not.
You would appear to be quite correct with the setting for the limits and homes - all should show port 1 pin 12, and all should have the "active low" box with a red cross - in other words the switches are active on a high voltage. Your switches are showing on, because pin 12 is not detecting a 0v signal.
The fact they are all showing "active" when they should be off means that (as in the safety case I mentioned earlier ) one of your switches could be faulty, or one of your wires could be loose, or one of the switches is connected the wrong way round, or the 0v return pin you have selected may not be connected internally in the computer, or to your break-out board if you have one.
As a "quicky" go into config and change one of the active high to an active low - and see if the corresponding LED on the dianostics page changes.
Make sure none of the switches are activated by the carriage.
Then connect a longish wire to a 0v terminal on your board - and, with the diagnostics page open, starting at pin 12, touch the wire onto pin 12 and see if the diagnostic page changes (a multi meter probe with a sharp point would be a good idea ). If it changes, then work from pin 12 backwards through the switches, checking with the 0v probe as each connection.
The LEDs should change as you "inject" the 0v - until you come to the faulty switch/wire/connection whatever.
On your system - all the LEDs will be lit or out simultaneously. Once you get them out, you are in business.
The three switches will work as limit switches in normal use - have a look at the instructional video about them - and how to configure the system so you can "back off" the switches if hit. If you ask the carriage to "home" the same switches are in use, but their method of working is changed by the computer, until the carriage is homed, and then they revert to limit switches.