Before RunWorkflow is called the interface changes directories to a 'workflow_run_dir' as defined in the ergatis.ini file. This is done because it writes temporary files in cwd that are removed once things finish.
I've never seen it, but apparently Worklow does the same thing when KillWorkflow is called, and we haven't set Ergatis to do the same directory change for this process.
1. This causes an error if the user apache is running as doesn't have write permissions to the CGI area.
2. The interface has no business writing in the CGI area. :)