I'd be very wary of making this judgement. (Unless you're a patent lawyer and this is your legal advice on this case, of course :-)
I also had a look at the DBIx::Chart homepage, and the text under "Show SQL" does look like SQL which produces graphs, complete with an addition to the SQL tokens ("RETURNING"). I think the patent is trying to claim such a kind of language.
I don't think that the DBIx::Chart implementation has any bearing. The patent claims a "system", and a system can be implemented in any number of peices.
I'm no lawyer, but prima facie I'd say that the patent and DBIx::Chart may be in conflict.
In reply to Re^2: Help! DBD/DBIx::Chart need patent protection!