You might want to watch the Homing, Limits and Offsets video.
http://www.machsupport.com/videos/Mach is always in G54 work offset unless you choose a different one. The offsets are relative to machine coordinates, which are defined when you ref the machine.
If you zero the regular DRO's and your project os offset from 0,0, then I'm guessing that the g-code is offset from 0,0. Can you post it?
I just did a quick test. Gcode for a circle centered at 0,0. Jog away from it. When I zero X and Y, the crosshairs center over the circle, at 0,0
Wwat you may need to do is regen the toolpath, as when you switch screens and change offsets and zero axis, the tolpath display may not be correct when you change back to a previous screen.
But watch the video. as Art does a pretty good job of explaining things.