AFAIK Samba doesn't do any conversion on line-endings. You're probably looking at a \r\n <-> \n conversion problem. As you (should) know Dos and NT use \r\n as end-of-line and Unix uses just \n.

Maybe you could use something like this (I never tried it though):

$/ = "\r\n";

while(<FILE>) {
   chomp;
   blabla;
}
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If this doesn't work you may want to open the file throug a dos2unix pipe:

open FILE, "dos2unix $file|" or die;
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