I have reinstalled WebBatch 3 times and have recreated the app in IIS at least 3 times, so I'm going to assume that this is an IIS configuration problem with the POST verb. There seem to be a lot of complaints in Google, but primarily with CGI/PHP GDI/Perl and the like. All of the cases I have looked at so far are not promising, since they all had typical sorts of configuration problems.
I also downloaded the latest version of WebBatch and got a temporary license so that I could try an install on a newer OS/IIS.
Regarding the IIS config not be saved, I have run into that before. There is a documented issue where the restart IIS option should not be used because sometimes it will terminate IIS before the configuration changes have been saved. The workaround is to stop the service from the Services management console and then to wait for it to stop before restarting the service. As long as I have been using that approach, I have not had any issues with lost configurations.