If you are manually modifying files outside of WordPress then BEFORE you turn AutoRestore back On you need to click the AutoRestore Backup Files button to make a new backup copy of the file you just modified. Since you are modifying a Root file outside of WordPress you would click the Root Files Backup Files button to create a new backup copy of the wp-config.php file that you modified. I actually find it simpler just to restore files from Quarantine instead of turning AutoRestore Off, backing up files and turning AutoRestore back On.
I guess you are seeing Control M characters because they were added somewhere in the process (Excel, Word or something else added them). Try this: Create new htaccess code using ONLY Notepad++ and you should not see Control M characters. Delete your old code because it has Control M characters and will always have Control M characters because they were added by something (Excel, Word or something else added them) in the process.