My problem is not exactly the same, but also uses the ftp-fileset protocol. The threads I have set up are supposed to process a file via a tcl proc and create a new file in a different directory and remove the old file, but sometimes the processing is not complete. Only part of the file is processed and the original file is deleted. When I requeue the file, the whole file is processed without any problems. The problem is usually caught because these are billing files and they get rejected when they are not complete. This problem has also been sporadic.
