Perl can handle the DOS line endings just fine, but as you said, it's the shell that can't (it tries to find a program named /usr/bin/perl^M to pass the script to). The cases you had where you didn't have issues with DOS line endings could have been that your #! line was something like: #!/usr/bin/perl -w^M, in which case the shell can find /usr/bin/perl and passes it the command line argument -w^M along with the script name, and perl can process those fine.