I am having a very simliar (if not the same) issue. I have written a JSFL script to loop through all the symbols in the library (only those of type=="movie clip" and with linkageExportForAS=true) and one at a time add them to the stage. At the bottom of the loop i do a selectAll() and deleteSelection() to clear the stage before moving on the the next symbol. When i run the script, it goes through the first 35 mc's just fine, but hits a snag on a particular symbol. When it snags, i get the warning/prompt "One or more library items already exist in the document." Normally this only occurs when you are pasting from one document/library to another. In this case, there is only one .fla open. I'm simply adding from the library to the stage. I would love to know what is happening, and why. I'd be happy not knowing but being able to handle this automatically, supress the dialog, auto select a choice, something to keep the script running. I'm not worried about replacing the symbol or not, as I know it isn't a new symbol, its just seems to be a bug. Maybe there is something wrong with the symbol, but I'm not the "owner" of the .fla, I'm just exporting PNG's of each keyframe of each symbol that has a "states" layer. So fixing the symbol isn't really an ideal solution. Maybe i can just catch the error, write an error file, and move on.
So, for any other poor chumps out there with the same problem, here's how i worked around it. This worked for my usage but probably wont for all cases... As I am looping through all items in the library, after i sort out the ones i want (movieclips with linkage) i create a duplicate symbol in the library, and give it a unique name. the duplicate method automatically appends a " copy", but as many unorganized libraries have symbols with similar names, i renamed it with a suffix of "_jsfl_copy". In addition, since the linkage was important to me, and duplicating an item does not copy the linkage values, I also had to manually turn linkage on and copy the values from the original item to the duplicated item. then i was able to add all the items to the stage without that prompt halting my jsfl script. Of course I removed the duplicate item at the bottom of my loop after i was done with it.