Basically, as long as you change both files to the same altitude ( the main AFCAD and the smaller one ), there shouldn't be an floating AI problem, that would only appear if you don't use the smaller file and change the altitude compared to the default one.
So, it's really doesn't matter which altitude you chose to use, since we are discussing about centimeters, it's not a big deal if the airport is set to an altitude 3-4 centimeters more than the real world, it never be realistic anyway, since no airport is really flat, and the published altitude it's just the one taken in the ARP reference point...whatever works for you, it's ok.
Yes, this could be hardware related, or more likely driver related. What affects the flickering at the driver level it's the Z-Buffer, the flickering happens because there's aren't enough bit used to get enough precision to represent altitude differences that small. Usually, you'd want to use a 32 bit Z-buffer, but made some research, and it seems some drivers cut corners and use a lower bit depth for the Z-buffer to get a performance boost, at the expense of image quality. In theory, WHQL certified drivers should have 24 bit z-buffer precision as minimum, but this might change between releases, tweaks, etc.
Note that, it's not possible to have a Z-buffer depth larger than the main color depth so, if you run FS9 in 16-bit color, it would have a worse 16 bit z-buffer too.
That might explain a difference in results between different systems.
