I said that you must be using NYTProf completely wrong because I don't think a module like this can break so spectacularly. Again, a wild guess :)
What is the commandline you used, or are you using NYTProf via Apache (i.e. How to use Devel::NYTProf on Apache)? Does NYTProf work without these problems on a different file?
For the particular log you provided, line 175 of /Devel/NYTProf/Reader.pm sets my $fname = $fi->filename_without_inc; and most of the complaints you see are saying that $fname is undefined. Why is that? Well it has something to do with that ->inc I guess again, because $fi->filename_without_inc must be somehow related? So there is no filename, there is no profile!
I propose that you restore NYTProf to its previous state (remove what I provided) and then if you want to debug, you must slowly work your way inside nytprofhtml and the modules it's using, inserting a print statement here or there. But first let's double check that the commandline is correct and that no ENV var is messing things up. Also make sure that NYTProf is properly installed by profiling a simple script and checking you get valid output.