Thanks for the spot, I missed that one. I remember something about needing to call ->init but when I reviewed the docs this seemed to indicate I didn't need to do anything more than load the module. I'll give that a shot. I've also been starting to use dtrace so it should be interesting to compare the results of the two.

The Apache::DProf module also requires apache version 1.3b3 or higher 
+and PerlChildInitHandler enabled. It is configured simply by adding t
+his line to your httpd.conf file:

 PerlModule Apache::DProf
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UPDATE - ->init didn't change anything, so it looks like that wasn't the issue. To convince myself that I was looking at valid results I created a subroutine:

sub sleepy {
  sleep 10;
}
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and I call sleepy() from My::Handler::handler. The ExclSec for My::Handler::handler is 10.47 seconds, and My::Handler::sleep is nowhere to be seen in the profile.