Use the "g" key to attack. When you get the pathing arrow, hover it over the AI unit. If it shows combat stats in the lower left then you know there are enemy units in that tile. If you don't see any stats, hover the pathing arrow in the surrounding areas.
Not familiar with "X-64". I did have some graphics improvements by downloading the most recent updates from windows. They also had new drivers for the on-board video set-up I have. That helped a bit as well.
I have seen units away from their flags before, but usually not very far. I also have seen misplaced health bars. Usually when I see the unit away from it's flag, it's right after combat and i had a sucessfull withdraw after attacking with fractional movement points. For example, I take my chariot and move across a river along a road and am left with .66 movement points. I might withdraw from combat, but my unit will be stuck in retreat and away from the flag. Which killing the AI unit with another unit reset the chariot graphic and it moved back under the flag with the actual unit.
The map border also has some graphic bugs in it regarding how units are displayed.
Another thing you might try is turning on the health bars. This might give you some hint as to where the baddies really are.
