I know this is an old thread, but this is a very real issue, and not the result of some authors and editors being clueless. Most of the journals and other publication guidelines in my field are standardized on American Antiquity style, which requires that works by the same author and year appear in the order cited in both the in-text citations and the references cited.
For example, (Smith 1997b) should not appear before Smith (1997a) in the text. If I cite Smitth (1997a) it should be the first “Smitth 1997” to be cited and it should also appear first in the bibliography, regardless of title alphabetization:
Rodgers, K. (2000) Some Great Stuff. Journal of Stuff 14:34-40.
Smith, J. (1997a) Better Living. Journal of Studies 54:1-4.
Smith, J. (1997b) Absolute Zero. Journal of Investigation 32:45-49.
Ubelaker, D. (1967) Old Fashioned Living. Journal of Studies 24:56-58.