Edit: I see now you mentioned this in your first post. Dammit, I never thought I'd be that guy.
You can use Pin to instrument your code with finer granularity. I think Pin would let you create a tool to count how many times you enter a function or how many clockticks you spend there, roughly emulating something like VTune or CodeAnalyst. Then you could strip down which functions get instrumented until your timing issues go away.