I sometimes get the same query from EndNote users, who are dismayed when they find that (Jones 2000b) occurs in the text before (Jones 2000a).
I explain to them that, in author-date referencing systems, the citation in the text is simply a way of locating an item in the reference list. The reference list is the hub of the referencing system, and the in-text citations correspond to the logical order of the entries in the reference list, which is arranged first by author, then by year, and finally by title.
All the standard referencing manuals follow this policy, including Chicago, APA and the (Australian) Style Manual for Authors, Editors and Printers (the “Snooks” manual).
Unfortunately there are quite a few dissertation supervisors and journal editors who are vague about referencing conventions! It takes some courage to tell them so…