Do not be ashamed for thinking Mach is complicated, it is. Especially if you are new to this. The mathematics, electronics, computers and then right when you think it is going to be easy, the difficulty of machining and materials jumps up. It is a challenge for sure.
Yes there are 2 settings for debounce. One is for spindle indexing. It is the interval setting you need. Place a number in the dialog box and press enter or it won't save. Though this setting will not cause a problem if you keep the numbers low as I suggested, the more I think about what you are saying. It appears more like the trigger isn't being recognized more than a false trip.
Regarding the ref boxes being green upon restart. In my experience they always are red upon start up, I then ref all ( in my understanding this gives a fresh point, removing any positional loss from previous runs and zeroes everything back out) then all turn green. I believe there is a setting on the general config page that will keep the settings constant when Mach shut downs but I have not had much luck yet. I in the name of safety and to minimize my tool loss find it easier to ref all at the beginning of the day and then proceed.
When you hit the machine coordinates button after a ref command (remember the ref all command should make the axis move until it hits the switch, it then sets all of the dros to zero) pressing the machine coordinates button again should give you your work offset if you had touched a piece you were going to work on. Machine coordinates should always be the same as this is telling you the limits of the physical machine. In truthfulness you can set this incorrectly but that is topic for later.
You mention that 3 of the 4 axis do ref correctly. Do you have a 4th axis? Does it have switches? Anyway does it do anything different if you press the ref all button on the main or program page?
One other thing if Hood contradicts anything I said. Follow his advice as he explains much clearer and knows much more than I.