[options=--valignmode=dot --graphstyle="anchor=base"]

(*)

and I didn't even noticed for a quite some time that this caused the
problem, the whole tex file was really not prepared and I was looking
at the old results.

Dot2tex(i) should provide some feedback to tex user that something is
going wrong not with tex but with embedded dot.

(*) I would be happy to know how to pass those arguments as well :-)

\begin{dot2tex}[options={--valignmode=dot --graphstyle="anchor=base"}]
...
\end{dot2tex}

The xkeyval parser gets confused when the option value contains and
equal sign(=). You therefore have to wrap the value in curly braces.

With dot2texi 3.0 you can also write:

\begin{dot2tex}[options={--valignmode=dot},graphstyle={anchor=base}]
...
\end{dot2tex}

I agree that dot2texi should give an error message when a dot2tex run
fails. I'll think about how to implement this.

By the way, The valign option will have no effect if you use the tikz
(default) output format.

Hope this helps!

Regards,
Kjell Magne Fauske