SOLVED

Thank you all for the suggestions and advice. I now know how to post properly for potential next posts.

The issue seems to have been the way I was viewing the output, and not a fault in the Perl script itself. I was viewing the output in the terminal (either by printing directly to STDOUT or by calling head on the output file) and somehow that created issues (missing tabs) that were not in the actual output file. I ended up downloading the output file locally and this showed that the file had all the required tabs.

Many thanks, and sorry for the multiple confusions. I really expected the issue to be a Perl one, not a matter of the way I was viewing the output.