John,
It should pick up changes in any include files that are part of the project itself. In other words, if the include file appears in the project tree, Simply Fortran should force a dependency on the file which included the modified INClude file.
If the include file is not part of the project, you have to disable the "project-includes-only" restriction. From the Options menu, select "Make and Makefile..." and uncheck the box labeled "Project-Only Fortran Include Dependencies." Simply Fortran should now pick up changes to any files that are INCLUDEd in Fortran source code.
If this option doesn't trigger the dependency, send along a snippet of code where the INCLUDE statement appears so I can have a look at whether a problem exists.
Jeff Armstrong
Approximatrix, LLC