I also am using perl on OS X and just did an experiment and was able to duplicate your problem.

If I saved the file in the old Mac format with ASCII CR's s as line separator, any comments in file would extend from the comment to EOF. But if I saved the file using ASCII LF's (\0x10) as line separator, everything worked as it should.

I believe you still have not succeeded in saving your file in unix format. Use hexdump to see exactly what line separator you have.