Tony,
I don't see a difference between your numbers and mine! (At least for the Sun, Earth, and Apophis)
But I still see the difference in the results.
I've attached my gsim file. It has the same objects as your A2004MN4.gsim, plus (1) I added a duplicate to Apophis called "New", which I then apply a series of thrusts to, and (2) I added Jupiter to see if that would help (it made no difference). It worked much as I thought, bringing Apophis close to the Moon in April of 2030. Then I tried to apply the latest numbers, and it doesn't work.
Note my simulation does turn on graphics and changes the focus and scale a couple of times. I generally start it, turn off graphics, and let it run until they turn back on by themselves around April 12, 2029, in time for the close approach. Incidentally, I'm mostly applying thrusts of the order of a few cm/s per month (things we can do with ion thrusters).
It's probably something simple and stupid I did, and can't see!
Also, I don't see where you get your numbers for the 2004MN4 January object, so it is simply wrong. At one point I just ran your model backward until 08-MAR-2028 and used those numbers, but somewhere I screwed that up.
And I still don't have the beta working. I was hoping a real "beta install" might help, although I don't see why!
Best regards,
Steve Covey
http://RamblingsOnTheFutureOfHumanity.com/