In regards to the first post, it appears that there is an undefined string being utilized when generating the flags during makefile construction if Aplot is linked. I'm mildly surprised it isn't crashing Simply Fortran. We had some changes in the Aplot flag generation due to macOS that caused this. I'll get new builds out today.
Line end characters are complicated. When a file is opened in Simply Fortran, it attempts to determine the line end characters predominantly in use in the file based on the first 20 or so lines of code. Regardless of the operating system, Simply Fortran will continue to use those line end characters that it thinks are the most common in the file from that point onwards. There probably could be a setting to force a given line end character, though.
But you've said that, when choosing "Windows Line End Characters," you receive a make error? Is that when the makefile is open? That setting in the Edit menu is per-file, meaning it only affects the currently open tab, nothing more. And unless you select "Convert All," it doesn't actually do anything until you press Enter in the editor.