I've had one report from a user saying that he couldn't display these characters at all - they only appear as boxes. It seems to me that the characters affected are just the ones that are displayed using the standard font without anti-aliasing. The user says that he can perfectly display these characters in other applications, so they must be available from the fonts. Since he tried out a variety of fontsets, it seems to be quite an issue...
The screenshot below shows croatian characters. Produce them by hitting the ] key (and neighbors) after M-x set-input-method croatian.
This happens on a CVS-derived, up-to-date Emacs on OS X 10.4.2.
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