I was working on TiVoToGo for my Series 3, too. I have the feeling that the TiVo Desktop software might be doing something funky with that directory. Try sharing a different directory and see if you can upload the files to it. Not that that will get your files to the TiVo, but it will take the TiVo Desktop software out of the picture altogether so you can see if it's the culprit.