The two output files show the results from -Tgif and -Tgif:gd. The two outputs are different. For the second node, even though both outputs use the same font, the glyphs are different.
The libgd behavior is identical using the Graphviz libgd and the
one on the system.
Input file: b1648.dot
Output file: b1648.gif
[erg] Comparing the Times-Roman nodes, where glyphs appear in both outputs, against the Unicode standard, it is clear that libgd is getting the correct glyphs and that cairo is putting up incorrect glyphs. Apparently, Vera.ttf does not have valid glyphs for those characters, hence the blanks.