The batch-upload function erroneously replaces the characters 3 and 9 with underscores. I have seen this bug reported on older versions of coppermine, but I have encountered it using the newest 1.4.9.
I fixed the problem by removing ' from 'forbiden_fname_char' in the config table. I know this is not the correct solution, but it works well enough for me. But it means that this bug is still not fixed for everybody.
I suspect, that the character encoding of the database could play a role in it. My Database (MySQL 3.32) uses iso-8859-1 and the other bug report I found was in the german forum (and he asked how to change to UTF-8). From this it is very likely, that he was also using the latin1 encoding. (http://forum.coppermine-gallery.net/index.php?topic=32459.msg151361#msg151361 (http://forum.coppermine-gallery.net/index.php?topic=32459.msg151361#msg151361)).
http://forum.coppermine-gallery.net/index.php?topic=25149.0