Bill = I'm not sure what you mean when you say a simulated run.
I load GCode into my office computer, and run it there - there is no machine attached - and the computer will run the code and show me the output on the tool display.
Or are you meaning the "simulate program run" on the toolpath display screen.
If you are saying that you run a program, without a machine atached, (which I suppose would be fairly simple if you were using "smooth stepper" or similar) and when you re-attach your machine the actual position does not correspond to the dro's, well, I don't think it will, or can do, because Mach is not controling the machine if it is only a simulation. To keep accurate position, Mach 3 needs to start at a known point, and then it adds, or subtracts all moves from its Machine Co-ordinates position.The program display which we tend to watch, is the same display, but with all the offsets disregarded, so it bears a resemblance to the GCode program.
You could write down your Machine Co-ordinates before and then type them into the DRO's afterwards, which would put the machine and computer back at the right "place" so to speak, but the problem would be that Mach would have different offsets, etc in it from the program you simulated - so although your Machine Co-ordinates were OK, your Program Co'ordinates could well be off.