There is a bug with the compiler optimization in previous releases that fails to re-compile libraries when #defines have changed within the main sketch source code files. 

This will affect projects such as Arducopter that reply on defines to control the functionality of various libraries.

This issue is resolved in the next release because the plugin defaults to re-compiling libraries if the sketch project macros are changed. 

If you are working entirely with libraries that are uneffected by macro changes then this feature can be disabled using "Project Properties>Macros Affect Libraries=False"
Workaround. In the current release, if you change #defines that libraries rely on you should disable (False) the "Tools>Options>Visual Micro>Compiler Optimisation>Library Modified" option.

When/if you finish changing #defines and have re-compiled, you can set it to true again.