diff --git a/cmd/syncthing/main.go b/cmd/syncthing/main.go
index 290ba719c..3dcfce8cd 100644
--- a/cmd/syncthing/main.go
+++ b/cmd/syncthing/main.go
@@ -344,7 +344,13 @@ func main() {
 
 	if options.confDir != "" {
 		// Not set as default above because the string can be really long.
-		baseDirs["config"] = options.confDir
+		if !filepath.IsAbs(options.confDir) {
+			path, err := filepath.Abs(options.confDir)
+			if err != nil {
+				l.Fatalln(err)
+			}
+			baseDirs["config"] = path
+		}
 	}
 
 	if err := expandLocations(); err != nil {
diff --git a/lib/model/model.go b/lib/model/model.go
index 9d7ab8877..273d3e7d5 100644
--- a/lib/model/model.go
+++ b/lib/model/model.go
@@ -285,7 +285,8 @@ func (m *Model) warnAboutOverwritingProtectedFiles(folder string) {
 		}
 
 		// check if file is ignored
-		if ignores.Match(protectedFilePath).IsIgnored() {
+		relPath, _ := filepath.Rel(folderLocation, protectedFilePath)
+		if ignores.Match(relPath).IsIgnored() {
 			continue
 		}