Perhaps a few more details are needed. Are you writing to the same file each time? If so, are you appending the new data to the file or overwriting the old data? If you're overwriting the old data then the file will always look as if only one of the instances of the program wrote to the file. Perhaps you are inadvertently overwriting the data.
If you're writing to different files how are you accomplishing this? Are you leaving the path empty so that the dialog box appears? If not, are you certain that the wiring is not such that you're actually overwriting the file?
There may be other causes which would be more clear if you posted some code which shows an example of what you're doing and where the problem exists.