If you use a system("ls -F > data") you will get the trailing \. Note that you will also get the other trailing symbols as well. The man page for "ls" excerpt:

-F    Marks directories with a  trailing  slash  (/),  doors
      with  a  trailing  greater-than  sign  (>), executable
      files with a  trailing  asterisk  (*),  FIFOs  with  a
      trailing  vertical  bar  (|),  symbolic  links  with a
      trailing at-sign (@), and AF_UNIX address family sockets
      with a trailing equals sign (=).
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I suspect that the user account you were using at the console has an alias in the startup files or is possibly defined at a higher system level to default the -F switch. I would think that you would be getting the same results if the latter were true or if you were logged in as the same user and performed both tasks.

Update: Hofmator is probably closer to the mark. i.e., -p instead of -F