I had the same problem. I set the days to remember incompleted files to 30. After that, files always disappeared in the Incomplete-folder after a while. Only small mp3-files was downloadable. Then I changed the days to remember incompleted files to 14 (two weeks). And then the problem disappeared! I don't know if this really was the reason, but if it is, the days to remember incomplete files must not be set too high.