You might give this thread a read. If it does not answer your issue, the topic requests that you post your message on it. Good luck and have a good evening.
Edit: I do have experience with my limit switches which I added to the Pro table back in November. One thing that really was important was to follow the warnings to update FireControl. Even if it is telling you to update to 1.5 even though you have 1.6, do it. Earlier this year that was an issue and I have not seen an explanation. What it did was updated to 1.5 and then when it restarted, nagged me to update to 1.6. I did both. You need to turn your machine off and then back on for everything to work right with the update when it is done.
Usually, people are reporting that the gantry is moving the wrong direction. That is when they are told to turn off the enclosure and start over and that seems to get everything in sync again.
If you are able to move X and Y with the typical FireControl keys, homing should go to the left back corner. If the limit switch failed to stop the movement, it is not working. While FireControl is active, just press one of the limit switches without asking it to home. That should throw an alarm. If it doesn’t, then you know the switch is not working (whether it is the switch, the wire or the connectors - you will need to sort thru that).