I can't provide a sscce because it's a very large module. I was using 6.05 but upgraded to 6.06 after your inquiry. It still fails with the same errors except one minor difference I don't understand (2695 -> 2698):

collapse_sibling_evals: nested evals in (eval 2695)
collapse_sibling_evals: nested evals in (eval 2698)

Debugging nytprof is over my head but I can see from the comments around line 430 in /Devel/NYTProf/FileInfo.pm that someone anticipated problems. How would you patch this?

# Should return the filename that the application used when loading th
+e file
# For evals should remove the @INC portion from within the "(eval N)[$
+path]"
# and similarly for Class::MOP #line evals "... defined at $path".
# This is a bit of a fudge. Filename handling should be improved in th
+e profiler.
sub filename_without_inc {
    my $self = shift;
    my $f    = [$self->filename];
    strip_prefix_from_paths([$self->profile->inc], $f, # line 430
        qr/(?: ^ | \[ | \sdefined\sat\s )/x
    );
    return $f->[0];
}
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