Ok - not sure what fixed it, the re-install, the patch, or playing back a mission to get a new save point, but we're back in the Big Chair again.
Got the ATI temporal AA working too. Mucho better. 1280x1024, effectively 8x AA, the graphics are as smooth as....well I don't want keep using that analogy. It only skips at those settings with a big explosion and multiple ships on screen.
It was nice to go back to the Dauntless missions for a bit, geez the Galaxy-class model is soooo much better looking than the Sov.
And now I can stop, I hope, randomly saying in Rainman style, "Data, yes. Go see Data."