That seems odd; an exposure is an exposure is an exposure. Could be a difference in the EV tables in the camera for the different modes.
I can verify when I get home (I have a couple of A-1 bodies and a 50L).
I was thinking it is possible that the camera or lens is malfunctioning mechanically, or the meter is simply not fast enough to respond during AE.
The FD, as you know, stops down to measure exposure during the exposure. If the lever that trips the aperture is not getting it all the way down before the measurement is made, it would be letting more light through than when on manual stop-down and manual metering. Alternatively, if the meter itself was not responding quickly enough - it might still be reacting to the light hitting it when it needed to report back a value and not yet have reached its final solution. Or the lens itself just might not be stopping down all the way when tripped automatically, but does when stopped down manually.
I don't know, just some thoughts.
The first thing I'd check would be a different lens on the same body. Then if I had a second body, I'd check that combination as well. Try to isolate it to a particular lens or a body.
I had an FL lens that would stop down manually properly, but when I tried to use it on my Canon FX (and FL body), in auto-stop down mode, it not stop down completely - the spring did not have enough tension. But the ring (some FL lenses had stop-down rings) did. So that's what made me think of it.