I use NYTProf often enough to have aliases set to maximize laziness:

alias profile='perl -d:NYTProf'
alias profileh='nytprofhtml --open'

That's been working for a very long time. I don't know how to use NYTProf wrong. It works well for me except for this one big module that does things which would cause modern PerlMonks to hide their children, but under strict conditions with no warnings, so I don't see why it upsets NYTProf.

I'm happy with the hack that gets me a report because I like to browse code as a website. Seeing it outside the comfort of my editor provides a different perspective. Maybe this thread will be useful to whoever adopts NYTProf and tries to improve filename handling of the profiler. Thanks for guessing :)