The only thing I can think of is that you haven't actually set the machine co-ordinates to 0.0 where you want home to be.
Machine co-ordinates and work co-ordinates are 2 separate things.
I'm a novice too and eventually found this out while using Mach3. I didn't realize about the differences until my table flew off my lil' X2 one day I don't have physical limits.
Just thought I'd mention it in case it is relevant.