as a newcomer to mach 3 and cnc, setting up the machine can be a minefield. There are so many options and cross options it's easy to get confused, so i would watch the first two tutorial videos, they have helped me so much and got me out of some wierd problems.
Take it in steps, get the movements in the right direction first with the dro going the right way, then sort out the home switches. Finally the soft limits, they never seem to work until everything is right.
I've converted a novamill and boxford 260 to mach3 over the last month or so and it's a great feeling when they do what you tell them.
You will get it sorted, and when you do you'll see where you went wrong and think, oh yeh i should have known that.