Strange. I have "A Final Unity" working (although with the ocassional flicker in the movies) in DosBox 0.70 without making any changes to the config file or running any extra utilities with it.
I'm not using DFend and I'm running through DOS4GW, as T5h suggested. I'm at a complete loss to figure out why it works for me like that, and not for you.
The only thing out of the ordinary I did was make the CD into an ISO because it was scratched and I was sick of the game stopping for 30 seconds whenever it needed anything from the CD.