I'm trying to use \beginpgfgraphicnamed to externalise some complex figures in a large document, using the latest released version of TiKZ (2.00). This produces standalone PDF images but for me the graphic is shifted up: the top part of the image is cut off and the bottom part has unnecessary whitespace. The overall PDF that is generated by pdflatex when these externalised images are used has the same visual problem, so I'm having to drop the idea of externalising graphics for now.
As far as I can tell the overall size of the pictures is correct (when comparing to the version without externalisation). I am using a custom thesis style file that changes margins, which is probably breaking several of the l2tabu no-no's.
How does PGF/TiKZ calculate the positioning of pictures on the page, at least as this affects positioning of externalised pictures?
In particular, are there specific things to tweak or to avoid tweaking to ensure this problem does not happen? I'm trying to not embark on a big LaTeX hacking project like redoing the style based on a more modern documentclass than report, so ways to steer clear of this would be especially welcome.