Note that taverna.dotlocation is read as a system properties instead of MyGridConfiguration.getProperty() by ScuflSVGDiagram and ScuflDiagramPanel.
This is to support setting taverna.dotlocation on the commandline, as now done in Windows (runme.bat) and in OS X (Taverna.app/blah/blah/Info.plist).
A better fix would be to let MyGridConfiguration.getProperties() to read overriden properties from system properties, like we do with raven.properties in Bootstrap. However, this causes a challenge as currently the MyGrid properties are also exported as system properties by loadMyGridProperties() for backward compatibility.
Possibly Graphviz should be an artifact with binaries included for known OS-es (also Linux), unpacked to some location (like .taverna/lib/graphviz), and run from there.
Solved by adding set ARGS=%ARGS% "-Dtaverna.dotlocation=%~dp0\bin\win32i386\dot.exe" using some 1337 windows batch scripting skillz. (%~dp0 is the path of the directory containing runme.bat)