With F4-AF and vista/win7, I recommend you install to root dir (C:\) or C:\games , don't install under C:\Programs\xxxx ,,,, .
Also check that graphic mode is set to D3d HAL , not T&L one .
Ed_1
Make sure F4-AF is patch to 1.0.13 as we added 8800 support around 1.0.10 or so.
Did you just add the 8800GT ?, was the previous vid card Nvidia, if so do a clean sweep of all Nvidia vid drivers and reload the 8800 ones, many times if not remove all older drivers it can cause issues.
Also try setting drivers setup to default, making sure FSAA and AA are set to application control, then see how it runs.
You should have no problems running this sim with your HW/OS.
Ed_1
F4-AF will run under Vista, but there is currently a transparency issue with ATI drivers and Vista.
We are currently in process of testing patch 1.13 which will fix this issue.
You can read some info here on it
http://www.lead-pursuit.com/news.htm
Ed_1