The log file is written into the "workspace". Until 2.9 the default workspace was indeed the working directory. This has caused problems when starting the GUI from an installation performed by an administrator because then the workspace inside the installation folder was not writable. Therefore we changed the location of the default workspace to the user's home directory. If you want different locations for different batch executions, you can specify the workspace location explicitly with the "-data" parameter.
does this "data" parameter still exist? Is its existence dependant on the system? Neither could I find it documented in the help nor was it mentioned when running the batch executor without parameters. And all possibilities I tried returned with an error that the parameter wasn't recognized...
-data is a standard parameter that works for every Eclipse application, see http://help.eclipse.org/indigo/index.jsp?topic=%2Forg.eclipse.platform.doc.isv%2Freference%2Fmisc%2Fruntime-options.html