May be a bit late to the party but thought I'd share my experience with the exact same problem...
I have a Asp.net Web MVC projcect that I had published to local IIS. After attempting to Attach my visual studio debugger to IIS process I was getting the same 'Breakpoint will not be hit' error, as well as having now project .dll file show in the Debug> Modules list.
My solution was a simple solution in the end but it turns out when I initially published the application to IIS local I had not selected the 'Debug configuration. Because of this I guess my visual studio debugger was never looking for the projects .dll file hence the reason not showing in the list.
I completely removed my app from my local IIS and re-published it using the Debug config rather than Release and it works...