I'm having the same issue as the user reporting this question on Stack Overflow, except in Visual Studio 2017 instead of 2015. When my solution is set to start multiple projects, only changes in one of them (and changes in dependencies) is being detected. I have to manually build the solution before running, or changes made to some of projects will not be compiled.
Everything works fine when the solution is set with a single startup project, but not with multiple. The default MsBuild process also picks up all changes correctly.