Has S3 upload support gone missing from the latest release of the Video module? We just updated to Video 7.x-2.6 and there's no sign of the Output file base field in the Transcoder tab. It was there when we were running an earlier dev release. All requirements (Libraries module, Zencoder php library, etc) are present and were working just fine prior to the video module upgrade.
I've found working with the video module to be more than a little frustrating because it seems to be a moving target, with outdated documentation. I'd be happy to contribute some time and write up some new docs, but I'm not even sure what featureset is currently supported.