This sounds eerily like a problem I encountered with dprof at DProf problem. At that time, there was no known cure (other than if you could track down where to add a commented out print statement with the right parameters:).

The best alternative was to use either Devel::SmallProf or Devel::Profiler.

I have had good results using the former and usually use it as a second pass after I have used DProf as it gives a line-by-line profile of the code rather than sub-by-sub which can be immensely useful.

I haven't managed to get Devel::Profiler to work for me, but it apparently has the advantage of not using the debugger interface (which the other 2 do) and so is less prone to 'upsetting' perl.