With 10.4 (Tiger), Apple has updated the 'unexpected quit' dialog which comes up after an app crashes. Usually the box offers a 'Reopen' button, which relaunches the app.
Sometimes, and it seems always with an AC crash, the button says 'try again' instead of 'reopen'. In this case there's some additional warning about 'settings'.
Today I tried the 'try again' button after an AC crash. When it relaunched I noticed the startup dialog had no recent files. Instead of going further I hit 'Quit AC'. After AC quit the system offered a dialog saying something to the effect of, 'the application's settings have changed, do you want to keep the new settings'. I said no. Then I relaunched AC normally, the startup dialog had recent files, and everything was fine.
It seems that 'try again' has an adverse impact on the preferences. I think had I proceeded to launch AC, or said 'yes' to the 'new settings' box, I would have wiped my prefs. Maybe further testing next time.
My advice is, where AC is concerned, ignore the friendly relaunch offer.