Jorge, was it the same with the D700?
On both my D700 and D3X using ZF (non-CPU) lenses, i have no problem whatsoever with A mode. Neither with AIS glass, in particular the supposedly problematic PCs. In the latter case the A mode is not suppposed to work (well it does, in some way) but the metering in M mode is ok.
AFAIK, there's no way to assign any further automatic settings to non-cpu lens except FL & min. aperture. But maybe our official documentalist and manual expert (Steen, you there?) will chime in. He'll know better.
Just in case, have you checked that when you "throw on the AIS lens", you're properly selecting the right lens/settings in the menu?
I'm sure you do, but it has happened to me before (typically when switching between 21/2.8 - 50/2 - 28/3.5).
Last but not least, which metering mode do you use with the AIS?
If you leave the Matrix mode on, it might explain some off metering. In most cases with AIS / non-CPU lenses, i use spot metering (with often double recompose, exposure, then focus, then actual framing, esp. for handheld landscapes). Center weighted should work fine, though.