As far as you mentioned earlier about changing the way the program writes, that solution would be up to you to research as this is a Perl forum. Otherwise, you could create a script that would translate the single line feed into what you want it to have.
ie:
Something like that, but for each line in the file. Is it the Unix version you want (single line feed) or the dos version (carraige return/line feed)? Either way, if unix2dos works for you, why not write a Perl script that utilizes it and simply feeds each file name through it?
Regards,
Jeff