diff --git a/autoload/syntastic/c.vim b/autoload/syntastic/c.vim
index 8d9ef73a..e49a29a0 100644
--- a/autoload/syntastic/c.vim
+++ b/autoload/syntastic/c.vim
@@ -223,24 +223,7 @@ function! s:_get_cflags(ft, ck, opts) abort " {{{2
 
     " check if the user manually set some cflags
     let b_cflags = s:_get_checker_var('b', a:ft, a:ck, 'cflags', '')
-    if b_cflags ==# ''
-        if a:ft ==# 'c' || a:ft ==# 'cpp'
-            " check whether to search for include files at all
-            if !s:_get_checker_var('g', a:ft, a:ck, 'no_include_search', 0)
-                " refresh the include file search if desired
-                if s:_get_checker_var('g', a:ft, a:ck, 'auto_refresh_includes', 0)
-                    let flags .= ' ' . s:_search_headers()
-                else
-                    " search for header includes if not cached already
-                    if !exists('b:syntastic_' . a:ft . '_includes')
-                        let b:syntastic_{a:ft}_includes = s:_search_headers()
-                    endif
-                    let flags .= ' ' . b:syntastic_{a:ft}_includes
-                endif
-            endif
-        endif
-    else
-        " user-defined cflags
+    if b_cflags !=# ''
         let flags .= ' ' . b_cflags
     endif
 
@@ -248,6 +231,19 @@ function! s:_get_cflags(ft, ck, opts) abort " {{{2
     let config_file = s:_get_checker_var('g', a:ft, a:ck, 'config_file', '.syntastic_' . a:ft . '_config')
     let flags .= ' ' . syntastic#c#ReadConfig(config_file)
 
+    if b_cflags ==# '' && (a:ft ==# 'c' || a:ft ==# 'cpp') && !s:_get_checker_var('g', a:ft, a:ck, 'no_include_search', 0)
+        " refresh the include file search if desired
+        if s:_get_checker_var('g', a:ft, a:ck, 'auto_refresh_includes', 0)
+            let flags .= ' ' . s:_search_headers()
+        else
+            " search for header includes if not cached already
+            if !exists('b:syntastic_' . a:ft . '_includes')
+                let b:syntastic_{a:ft}_includes = s:_search_headers()
+            endif
+            let flags .= ' ' . b:syntastic_{a:ft}_includes
+        endif
+    endif
+
     return flags
 endfunction " }}}2
 
diff --git a/plugin/syntastic.vim b/plugin/syntastic.vim
index 98602f58..13db02d0 100644
--- a/plugin/syntastic.vim
+++ b/plugin/syntastic.vim
@@ -19,7 +19,7 @@ if has('reltime')
     lockvar! g:_SYNTASTIC_START
 endif
 
-let g:_SYNTASTIC_VERSION = '3.6.0-140'
+let g:_SYNTASTIC_VERSION = '3.6.0-141'
 lockvar g:_SYNTASTIC_VERSION
 
 " Sanity checks {{{1