I am using the following command in both the cases

perltidy -html test.pl -frames
[download]

As you might be already knowing perltidy implicitly calls pod2html. Anyways I tried calling pod2html directly too with no change
I can paste the code here tomorrow if you want. But as I said in the above post, I have put both the POD sections(with same text) in one script and then ran it to get different results.