Try re-installing ioNiNJA in the scripts directory and use the default settings just to see if it works.
My guess is some option/configuration setting is causing an error to show up that most users aren't seeing. Whenever there is an error returned to ioFTPD the server deletes the file because a non-success return code means something was wrong with the uploaded file.
If it works with the default settings, go ahead and re-apply some of the settings until it breaks again so you can figure out which option is causing the problem.
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