The last 4 sets of includes are equivalent. You should only keep one (${workspaceFolder}/**). You should also omit the -I when specifying includes since you are using fortran.linter.includePaths
Update to pre-release of the extension and set fortran.logging.level to DEBUG. Then post the output from the OUTPUT pane > Modern Fortran.
I will have a more detailed look in your settings later, but here is a link to the fortls docs for source file parsing which you might find useful
https://fortls.fortran-lang.org/options.html#sources-file-parsing