diff --git a/development.ini b/development.ini
--- a/development.ini
+++ b/development.ini
@@ -386,9 +386,8 @@ keys = generic, color_formatter, color_f
 [logger_root]
 level = NOTSET
 #handlers = console
+## For coloring based on log level:
 handlers = console_color
-## For coloring based on log level:
-#handlers = console_color
 
 [logger_routes]
 #level = WARN
diff --git a/kallithea/lib/inifile.py b/kallithea/lib/inifile.py
--- a/kallithea/lib/inifile.py
+++ b/kallithea/lib/inifile.py
@@ -103,20 +103,17 @@ def expand(template, mako_variable_value
     # option a was chosen
     <BLANKLINE>
     [comment-section]
-    #variable3 = 3.0
+    variable3 = 3.0
     #variable4 = 4.0
+    variable4 = 4.1
     #variable5 = 5.0
     #variable5 = 5.1
     variable5 = 5.2
     #variable6 = 6.0
     #variable6 = 6.1
-    #variable7 = 7.0
-    #variable7 = 7.1
+    variable6 = 6.2
     variable7 = 7.0
-    <BLANKLINE>
-    variable3 = 3.0
-    variable4 = 4.1
-    variable6 = 6.2
+    #variable7 = 7.1
     <BLANKLINE>
     [fourth-section]
     fourth = "four"
@@ -143,20 +140,44 @@ def expand(template, mako_variable_value
         sectionname, lines = m.groups()
         if sectionname in settings:
             section_settings = settings.pop(sectionname)
+            add_after_key_value = {}  # map key to value it should be added after
 
-            def process_line(m):
-                """process a section line and update value if necessary"""
-                key, value = m.groups()
+            # 1st pass:
+            # comment out lines with keys that have new values
+            # find best line for keeping or un-commenting (because it has the right value) or adding after (because it is the last with other value)
+            def comment_out(m):
+                """process a section line if in section_settings and comment out and track in add_after_key_value"""
                 line = m.group(0)
-                if key in section_settings:
-                    new_line = '%s = %s' % (key, section_settings.pop(key))
-                    if new_line != line:
-                        # keep old entry as example - comments might refer to it
-                        line = '#%s\n%s' % (line, new_line)
-                return line.rstrip()
+                comment, key, line_value = m.groups()
+                if key not in section_settings:
+                    return line
+                new_value = section_settings[key]
+                if line_value == new_value or add_after_key_value.get(key) != new_value:
+                    add_after_key_value[key] = line_value
+                if comment:
+                    return line
+                return '#' + line
+
+            lines = re.sub(r'^(#)?([^#\n\s]*)[ \t]*=[ \t]*(.*)$', comment_out, lines, flags=re.MULTILINE)
 
-            # process lines that not are comments or empty and look like name=value
-            lines = re.sub(r'^([^#\n\s]*)[ \t]*=[ \t]*(.*)$', process_line, lines, flags=re.MULTILINE)
+            def add_after_comment(m):
+                """process a section comment line and add new value"""
+                line = m.group(0)
+                key, line_value = m.groups()
+                if key not in section_settings:
+                    return line
+                if line_value != add_after_key_value.get(key):
+                    return line
+                new_value = section_settings[key]
+                if new_value == line_value:
+                    line = line.lstrip('#')
+                else:
+                    line += '\n%s = %s' % (key, new_value)
+                section_settings.pop(key)
+                return line
+
+            lines = re.sub(r'^#([^#\n\s]*)[ \t]*=[ \t]*(.*)$', add_after_comment, lines, flags=re.MULTILINE)
+
             # add unused section settings
             if section_settings:
                 lines += '\n' + ''.join('%s = %s\n' % (key, value) for key, value in sorted(section_settings.items()))