GUI version of Emacs doesn't display all glyphs available in font

[Teemu Likonen]

My problems is that the GUI Emacs doesn't render all glyphs correctly.
In some situations certain characters are rendered as squares while
XTerm renders them correctly. I use exactly the same font in XTerm and
Emacs (GUI). The font is:

    -misc-fixed-medium-r-normal--18-120-100-100-c-90-iso10646-1

Here's an example: With the mentioned font and with Emacs inside XTerm
the command

    C-h C-\ ipa RET             ; (describe-input-method 'ipa)

displays correctly all except five characters. The glyphs of those five
characters are most likely missing from the font. But inside GUI Emacs
every single one of those IPA characters are rendered as squares. If I
use ipa input method to actually insert those characters to a buffer,
they show just fine.

Sometimes I see squares in Gnus *Article* buffer in other people's
messages, but those characters show just fine if I copy&paste them from
GUI Emacs to XTerm window. At least U+6EC1 is one of them.

So, I suspect that GUI Emacs (or Fontconfig or something) tries to
display those characters with another font. If this is the problem how
can I make GUI Emacs use my -misc-fixed-* font? I know it has a good
coverage of glyphs.