HA! The cardboard developer strikes again!
One additional complication in my particular scenario is that my compiled application isn't in the usual bin\Debug
locations. Each project copies itself and any dependencies into a completely separate location (kind of like deployment I guess) and then executed from there when I debug.
What I've done to get this working:
The usual nasty post signing shenanigans to get the strong names to play nicely
Instead of going through the wizard simply click Start Performance Analysis under the Analyze menu
This will start the performance analysis and should honour any debug setup in your start up projects properties page.
Go back to the Visual Studio 2012/2013 instance you started from.
Right-click on the Targets node in the Performance Explorer panel.
Select Add Target Binary and then in the file browser select the compiled modules that form the composited parts of your application
Run your app as you wish and then select Stop Profiling when you're done.
Explore to see just how crap your code is! :)
NB: last step is optional.