diff --git a/include/Makefile.in b/include/Makefile.in
index d03c6d9412a..d5f389b506a 100644
--- a/include/Makefile.in
+++ b/include/Makefile.in
@@ -429,6 +429,7 @@ SOURCES = \
 	mimeole.idl \
 	minidumpapiset.h \
 	minmax.h \
+	minschannel.h \
 	mlang.idl \
 	mmc.idl \
 	mmddk.h \
diff --git a/libs/faudio/Makefile.in b/libs/faudio/Makefile.in
index 3a9bb591227..639cd2cbff0 100644
--- a/libs/faudio/Makefile.in
+++ b/libs/faudio/Makefile.in
@@ -1,5 +1,5 @@
 EXTLIB    = libfaudio.a
-EXTRAINCL = -I$(srcdir)/include
+EXTRAINCL = $(FAUDIO_PE_CFLAGS)
 EXTRADEFS = -DFAUDIO_WIN32_PLATFORM -DHAVE_WMADEC -DNDEBUG
 
 C_SRCS = \
diff --git a/libs/gsm/Makefile.in b/libs/gsm/Makefile.in
index 36c749aa60f..d2aefc937f9 100644
--- a/libs/gsm/Makefile.in
+++ b/libs/gsm/Makefile.in
@@ -1,5 +1,5 @@
 EXTLIB    = libgsm.a
-EXTRAINCL = -I$(srcdir)/inc
+EXTRAINCL = $(GSM_PE_CFLAGS)
 EXTRADEFS = -DWAV49
 
 C_SRCS = \
diff --git a/libs/jxr/Makefile.in b/libs/jxr/Makefile.in
index 5203dc970aa..3162cfca263 100644
--- a/libs/jxr/Makefile.in
+++ b/libs/jxr/Makefile.in
@@ -1,5 +1,6 @@
 EXTLIB    = libjxr.a
-EXTRAINCL = -I$(srcdir)/jxrgluelib -I$(srcdir)/image/sys -DDISABLE_PERF_MEASUREMENT
+EXTRAINCL = $(JXR_PE_CFLAGS)
+EXTRADEFS = -DDISABLE_PERF_MEASUREMENT
 
 C_SRCS = \
 	image/decode/JXRTranscode.c \
diff --git a/libs/lcms2/Makefile.in b/libs/lcms2/Makefile.in
index 6549d5718b5..c2aafa9c70a 100644
--- a/libs/lcms2/Makefile.in
+++ b/libs/lcms2/Makefile.in
@@ -1,5 +1,5 @@
 EXTLIB    = liblcms2.a
-EXTRAINCL = -I$(srcdir)/include
+EXTRAINCL = $(LCMS2_PE_CFLAGS)
 
 C_SRCS = \
 	src/cmsalpha.c \
diff --git a/libs/mpg123/Makefile.in b/libs/mpg123/Makefile.in
index 6859f66f68a..7974c34ed91 100644
--- a/libs/mpg123/Makefile.in
+++ b/libs/mpg123/Makefile.in
@@ -1,5 +1,5 @@
 EXTLIB    = libmpg123.a
-EXTRAINCL = -I$(srcdir)/src -I$(srcdir)/src/compat -I$(srcdir)/src/libmpg123
+EXTRAINCL = -I$(srcdir)/src -I$(srcdir)/src/compat $(MPG123_PE_CFLAGS)
 EXTRADEFS = -DOPT_GENERIC_DITHER -DREAL_IS_FLOAT -DNO_CATCHSIGNAL -DMPG123_NO_LARGENAME
 
 C_SRCS = \
diff --git a/libs/tiff/Makefile.in b/libs/tiff/Makefile.in
index f8ceb5006d4..7c793f3e2f9 100644
--- a/libs/tiff/Makefile.in
+++ b/libs/tiff/Makefile.in
@@ -1,5 +1,5 @@
 EXTLIB    = libtiff.a
-EXTRAINCL = -I$(srcdir)/libtiff $(JPEG_PE_CFLAGS) $(ZLIB_PE_CFLAGS)
+EXTRAINCL = $(TIFF_PE_CFLAGS) $(JPEG_PE_CFLAGS) $(ZLIB_PE_CFLAGS)
 
 C_SRCS = \
 	libtiff/tif_aux.c \
diff --git a/libs/vkd3d/Makefile.in b/libs/vkd3d/Makefile.in
index c912f97165e..0ed4e27ad83 100644
--- a/libs/vkd3d/Makefile.in
+++ b/libs/vkd3d/Makefile.in
@@ -1,5 +1,5 @@
 EXTLIB    = libvkd3d.a
-EXTRAINCL = -I$(srcdir)/include -I$(srcdir)/include/private -I$(srcdir)/libs/vkd3d -I$(srcdir)/libs/vkd3d-shader
+EXTRAINCL = $(VKD3D_PE_CFLAGS) -I$(srcdir)/include/private -I$(srcdir)/libs/vkd3d -I$(srcdir)/libs/vkd3d-shader
 EXTRADEFS = \
 	-DWINE_NO_NAMELESS_EXTENSION \
 	-DCONST_VTABLE \
diff --git a/tools/makedep.c b/tools/makedep.c
index 81e9c20fd4f..fb09e6acc8a 100644
--- a/tools/makedep.c
+++ b/tools/makedep.c
@@ -4152,10 +4152,20 @@ static void load_sources( struct makefile *make )
 
     value = get_expanded_make_var_array( make, "EXTRAINCL" );
     for (i = 0; i < value.count; i++)
+    {
         if (!strncmp( value.str[i], "-I", 2 ))
-            strarray_add_uniq( &make->include_paths, value.str[i] + 2 );
+        {
+            const char *dir = value.str[i] + 2;
+            if (!strncmp( dir, "./", 2 ))
+            {
+                dir += 2;
+                while (*dir == '/') dir++;
+            }
+            strarray_add_uniq( &make->include_paths, dir );
+        }
         else if (!strncmp( value.str[i], "-D", 2 ) || !strncmp( value.str[i], "-U", 2 ))
             strarray_add_uniq( &make->define_args, value.str[i] );
+    }
     strarray_addall( &make->define_args, get_expanded_make_var_array( make, "EXTRADEFS" ));
 
     strarray_add( &make->include_args, strmake( "-I%s", obj_dir_path( make, "" )));