This is not proper behavior. ltg can help you a lot better than I can, but the switches need to be CLOSED normally.
I misspoke earlier; the matrix should show the switches a darker blue than the rest of the switches (meaning inactive normally-closed non-opto), then turn green when you hit the target (opening the switch, causing it to be "active" in this case). The action of pushing on the witch target should cause the arm of the micro switch to not activate anymore.
It's at least POSSIBLE your switches are wired normally-closed (I have never seen any microswitch wired this way on purpose in all my years of designing games as far as I recall) which would also cause the reverse action you are encountering.
The diode should be soldered to the outside lugs, with the band pointing to the lug where the pivot is. The green-x wire should be soldered to the middle lug. The white-x wire should be soldered to the lug away from the pivot point.