More on "JS alert that links to file"

I have a question that follows on from this discussion. I have a loop which creates a number of files. It first write each file to a server location then sets up the headers and asks the "Save As" question. This works OK once, but after the first download it exits without any errors or messages. If I remove the header() lines (ie just create the files on the server) no worries, it creates them all. (I start op buffer at the top of the code and flush the buffer on each loop). Anyone have any ideas please? Thanks Tony