diff --git a/ChangeLog b/ChangeLog
index c336f4645..9057e2f3d 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,11 @@
+2011-02-06  Moritz Bunkus  <moritz@bunkus.org>
+
+	* build system: Fixed compilation if configure choses the internal
+	versions of libebml and libmatroska while older versions are still
+	installed in a location named with "-I..." or "-L..." in
+	CFLAGS/CXXFLAGS/LDFLAGS or with configure's
+	"--with-extra-includes" and "--with-extra-libs" options.
+
 2011-01-31  Moritz Bunkus  <moritz@bunkus.org>
 
 	* Released v4.5.0.
diff --git a/Rakefile b/Rakefile
index a074aa6ea..876d04708 100644
--- a/Rakefile
+++ b/Rakefile
@@ -78,13 +78,13 @@ def setup_globals
 
   $build_tools           ||=  c?(:TOOLS)
 
-  cflags_common            = "-Wall -Wno-comment #{c(:OPTIMIZATION_CFLAGS)} -D_FILE_OFFSET_BITS=64 #{c(:EXTRA_CFLAGS)} #{c(:DEBUG_CFLAGS)} #{c(:PROFILING_CFLAGS)} #{c(:MATROSKA_CFLAGS)} #{c(:EBML_CFLAGS)} #{c(:USER_CPPFLAGS)} -DPACKAGE=\\\"#{c(:PACKAGE)}\\\" -DVERSION=\\\"#{c(:VERSION)}\\\" -DMTX_LOCALE_DIR=\\\"#{c(:localedir)}\\\" -DMTX_PKG_DATA_DIR=\\\"#{c(:pkgdatadir)}\\\" -DMTX_DOC_DIR=\\\"#{c(:docdir)}\\\""
+  cflags_common            = "-Wall -Wno-comment #{c(:OPTIMIZATION_CFLAGS)} -D_FILE_OFFSET_BITS=64 #{c(:MATROSKA_CFLAGS)} #{c(:EBML_CFLAGS)} #{c(:EXTRA_CFLAGS)} #{c(:DEBUG_CFLAGS)} #{c(:PROFILING_CFLAGS)} #{c(:USER_CPPFLAGS)} -DPACKAGE=\\\"#{c(:PACKAGE)}\\\" -DVERSION=\\\"#{c(:VERSION)}\\\" -DMTX_LOCALE_DIR=\\\"#{c(:localedir)}\\\" -DMTX_PKG_DATA_DIR=\\\"#{c(:pkgdatadir)}\\\" -DMTX_DOC_DIR=\\\"#{c(:docdir)}\\\""
   ldflags_extra            = c?(:MINGW) ? '' : "-Wl,--enable-auto-import"
   $flags                   = {
     :cflags                => "#{cflags_common} #{c(:USER_CFLAGS)}",
     :cxxflags              => "#{cflags_common} #{c(:WXWIDGETS_CFLAGS)} #{c(:QT_CFLAGS)} #{c(:BOOST_CPPFLAGS)} #{c(:CURL_CFLAGS)} #{c(:USER_CXXFLAGS)}",
     :cppflags              => "#{c(:USER_CPPFLAGS)}",
-    :ldflags               => "#{c(:EXTRA_LDFLAGS)} #{c(:PROFILING_LIBS)} #{c(:USER_LDFLAGS)} #{c(:LDFLAGS_RPATHS)} #{c(:BOOST_LDFLAGS)}",
+    :ldflags               => "#{c(:EBML_LDFLAGS)} #{c(:MATROSKA_LDFLAGS)} #{c(:EXTRA_LDFLAGS)} #{c(:PROFILING_LIBS)} #{c(:USER_LDFLAGS)} #{c(:LDFLAGS_RPATHS)} #{c(:BOOST_LDFLAGS)}",
   }
 end
 
diff --git a/ac/ebml.m4 b/ac/ebml.m4
index 56ffdd8fb..24e4de7aa 100644
--- a/ac/ebml.m4
+++ b/ac/ebml.m4
@@ -1,5 +1,5 @@
 dnl
-dnl Test for libebml, and define EBML_CFLAGS and EBML_LIBS
+dnl Test for libebml, and define EBML_CFLAGS, EBML_LDFLAGS and EBML_LIBS
 dnl
   ebml_ver_req_major=1
   ebml_ver_req_minor=2
@@ -29,7 +29,8 @@ using namespace libebml;
 
     if test "${ac_cv_ebml_found}" = "no" ; then
       EBML_CFLAGS="-I/usr/local/include"
-      EBML_LIBS="-L/usr/local/lib $EBML_LIBS"
+      EBML_LDFLAGS="-L/usr/local/lib"
+      EBML_LIBS="$EBML_LIBS"
       CXXFLAGS="-I/usr/local/include $CXXFLAGS"
       LIBS="-L/usr/local/lib $LIBS"
       AC_TRY_COMPILE([
@@ -58,7 +59,8 @@ using namespace libebml;
 
   if test x"${ac_cv_ebml_found}" = "xinternal" ; then
     EBML_CFLAGS="-Ilib/libebml"
-    EBML_LIBS="-Llib/libebml/src -lebml"
+    EBML_LDFLAGS="-Llib/libebml/src"
+    EBML_LIBS="-lebml"
 
   else
 dnl
@@ -73,7 +75,7 @@ dnl
         ac_save_CXXFLAGS="$CXXFLAGS"
         ac_save_LIBS="$LIBS"
         CXXFLAGS="$CXXFLAGS $EBML_CFLAGS"
-        LIBS="$LIBS $EBML_LIBS"
+        LIBS="$LIBS $EBML_LDFLAGS $EBML_LIBS"
         AC_TRY_LINK([
 #include <ebml/EbmlVersion.h>
 #include <ebml/EbmlDummy.h>
@@ -113,4 +115,5 @@ using namespace libebml;
   fi
 
 AC_SUBST(EBML_CFLAGS)
+AC_SUBST(EBML_LDFLAGS)
 AC_SUBST(EBML_LIBS)
diff --git a/ac/matroska.m4 b/ac/matroska.m4
index 96acfc586..29286cc7e 100644
--- a/ac/matroska.m4
+++ b/ac/matroska.m4
@@ -1,5 +1,5 @@
 dnl
-dnl Test for libmatroska, and define MATROSKA_CFLAGS and MATROSKA_LIBS
+dnl Test for libmatroska, and define MATROSKA_CFLAGS, MATROSKA_LDFLAGS and MATROSKA_LIBS
 dnl
   kax_ver_req_major=1
   kax_ver_req_minor=1
@@ -34,7 +34,8 @@ using namespace libmatroska;
 
       if test x"${ac_cv_matroska_found}" != "xyes" ; then
         MATROSKA_CFLAGS="-I/usr/local/include"
-        MATROSKA_LIBS="-L/usr/local/lib $MATROSKA_LIBS"
+        MATROSKA_LDFLAGS="-L/usr/local/lib"
+        MATROSKA_LIBS="$MATROSKA_LIBS"
         CXXFLAGS="-I/usr/local/include $CXXFLAGS"
         LIBS="-L/usr/local/lib $LIBS"
         AC_TRY_COMPILE([
@@ -67,7 +68,8 @@ using namespace libmatroska;
     EBML_CFLAGS="-Ilib/libebml"
     EBML_LIBS="-Llib/libebml/src -lebml"
     MATROSKA_CFLAGS="-Ilib/libmatroska"
-    MATROSKA_LIBS="-Llib/libmatroska/src -lmatroska"
+    MATROSKA_LDFLAGS="-Llib/libmatroska/src"
+    MATROSKA_LIBS="-lmatroska"
     EBML_MATROSKA_INTERNAL=yes
 
   else
@@ -80,7 +82,7 @@ using namespace libmatroska;
         ac_save_CXXFLAGS="$CXXFLAGS"
         ac_save_LIBS="$LIBS"
         CXXFLAGS="$CXXFLAGS $EBML_CFLAGS $MATROSKA_CFLAGS"
-        LIBS="$LIBS $MATROSKA_LIBS $EBML_LIBS"
+        LIBS="$LIBS $MATROSKA_LDFLAGS $MATROSKA_LIBS $EBML_LIBS"
         AC_TRY_LINK([
 #include <matroska/KaxVersion.h>
 #include <matroska/KaxSegment.h>
@@ -124,5 +126,6 @@ using namespace libmatroska;
   fi
 
 AC_SUBST(MATROSKA_CFLAGS)
+AC_SUBST(MATROSKA_LDFLAGS)
 AC_SUBST(MATROSKA_LIBS)
 AC_SUBST(EBML_MATROSKA_INTERNAL)
diff --git a/build-config.in b/build-config.in
index 667fa6f10..71dfb4586 100644
--- a/build-config.in
+++ b/build-config.in
@@ -74,6 +74,7 @@ DEBUG_CFLAGS = @DEBUG_CFLAGS@
 DOCBOOK_MANPAGES_STYLESHEET = @DOCBOOK_MANPAGES_STYLESHEET@
 DOCBOOK_ROOT = @DOCBOOK_ROOT@
 EBML_CFLAGS = @EBML_CFLAGS@
+EBML_LDFLAGS = @EBML_LDFLAGS@
 EBML_LIBS = @EBML_LIBS@
 EBML_MATROSKA_INTERNAL = @EBML_MATROSKA_INTERNAL@
 EGREP = @EGREP@
@@ -88,6 +89,7 @@ LIBINTL_LIBS = @LIBINTL_LIBS@
 LZO_LIBS = @LZO_LIBS@
 MAGIC_LIBS = @MAGIC_LIBS@
 MATROSKA_CFLAGS = @MATROSKA_CFLAGS@
+MATROSKA_LDFLAGS = @MATROSKA_LDFLAGS@
 MATROSKA_LIBS = @MATROSKA_LIBS@
 MINGW_GUIAPP = @MINGW_GUIAPP@
 MINGW_LIBS = @MINGW_LIBS@