When it says Major at 11:45 - 1:45 what is the best fishing time? Before 11:45 or after 1:45?

When it says Major, then that's the best time. The two times mean from - to.
So in your case you should go fishing from 11:45 until 1:45 and not before or after

Same with Minor - they are the second best times in a day.

That's the best time to fish is in between the times. Not saying fish won't be caught at other times but that's the main feeding times. Same as with minor. Between those timelines are the least you might get bit.

Just want to confirm, so is the Minor time the times that you will most probably not catch anything or is it the second best time to fish?

What if it's flat --- on the major time?

yeah - minor times are the second best times.
Sometimes they can be just as good as major times, depending on your location, weather, tides etc.

With the major and minor times you got 4 good fishing periods in each day.

you mean flat tide? Give it a try. It works for me even on dead low or dead high tide.
Quite often the current picks up during the fishing times and fish are already hungry.