Assuming that you are having Windchill on a Unix box and CAD worker on Windows box, PTC recommends configuring FTP on Windows using IIS configuration. There had been other methods identified for setting up FTP for publishing other than IIS, but unfortunately those are not supported by PTC. Regarding your server failure you may want to narrow down to the root cause or I would suggest reconfigure a fresh FTP all over again and monitor the situation.
