perl5 Number Sign # not working for comments

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I have a very strange problem..

perl5 Number Sign # not working correctly for comments..

We use emperl, mod_perl, apache, linux..

In some programs if I have a line commented out with a number sign # or just a number sign # by itself on a line, all of the code below that line doesn't work correctly.

There is a sysadmin so I don't have access or control over any of the settings on the server.

This is a new issue everything always worked previously.

So many possible area's that this might be coming from that I'm checking to see if anybody has run across this..

Any suggestions?

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Found the issue:

Was transferring the files from LINUX to Windows to edit them.

If the file was originally created in Windows the end of a line was just a <CR> and for some reason the whole file wasn't running right. It mainly showed up when using the hash symbol for perl comments.

When I made sure the files had end of lines with <CR><LF>, this solved this issue.