The FileDocument entity comes with a DeleteAfterDownload boolean that defaults to false. Do you happen to be adjusting this value?
We had the same problem (Modeler 126.96.36.199). It was caused by the property MaxFileSize. All uploaded files larger then the default 5Mb (MaxFileSize) couldn't be downloaded. maybe it's the same issue in 2.5.3. Just increase the maxFileSize property.
Do you commit the object you create your document in?