diff --git a/README.MinGW b/README.MinGW
index cdc061a93..6066e1514 100644
--- a/README.MinGW
+++ b/README.MinGW
@@ -26,9 +26,13 @@ To build the source distribution under MSYS follow these steps:
     and the following MSYS packages:
       * MSYS-1.0.10.exe
       * msysDTK-1.0.1.exe
+      * msys-autoconf-2.59.tar.bz2
     Later versions of the above packages may also work, but earlier versions
     should be avoided.
     
+    You also need to download and install the flex and bison packages
+    from GnuWin32 <http://sourceforge.net/projects/gnuwin32/>.
+
 2.  Open an MSYS session and unpack the source distribution with a command 
     like:
     
diff --git a/configure.in b/configure.in
index 8da648e69..8aa3f93a6 100644
--- a/configure.in
+++ b/configure.in
@@ -31,19 +31,22 @@ AC_PREREQ(2.58)
 # The environment variable `SUPPRESS_LOG_FILE_RECURSION' is used to prevent
 # infinite recursion.
 #
-if test "$SUPPRESS_LOG_FILE_RECURSION" != "yes"; then
-	SUPPRESS_LOG_FILE_RECURSION=yes
-	export SUPPRESS_LOG_FILE_RECURSION
-	trap 0 1 2 3 13 15
-	rm -f configure.exit_status
-	{ case $# in
-		0) ${CONFIG_SHELL-/bin/sh} "$0"      ;;
-		*) ${CONFIG_SHELL-/bin/sh} "$0" "$@" ;;
-	esac; echo $? > configure.exit_status; } | exec tee configure.log
-	status=`cat configure.exit_status`
-	rm -f configure.exit_status
-	exit $status
-fi
+
+# XXX Currently this is commented out because autoconf 2.60 breaks
+# how this works.
+#if test "$SUPPRESS_LOG_FILE_RECURSION" != "yes"; then
+#	SUPPRESS_LOG_FILE_RECURSION=yes
+#	export SUPPRESS_LOG_FILE_RECURSION
+#	trap 0 1 2 3 13 15
+#	rm -f configure.exit_status
+#	{ case $# in
+#		0) ${CONFIG_SHELL-/bin/sh} "$0"      ;;
+#		*) ${CONFIG_SHELL-/bin/sh} "$0" "$@" ;;
+#	esac; echo $? > configure.exit_status; } | exec tee configure.log
+#	status=`cat configure.exit_status`
+#	rm -f configure.exit_status
+#	exit $status
+#fi
 
 #-----------------------------------------------------------------------------#
 # Work out the default arguments to configure when reconfiguring,
@@ -932,7 +935,7 @@ mercury_check_for_functions \
 		getpid setpgid fork execlp wait kill \
 		grantpt unlockpt ptsname tcgetattr tcsetattr ioctl \
 		access sleep opendir readdir closedir mkdir symlink readlink \
-		gettimeofday
+		gettimeofday setenv putenv _putenv
 
 #-----------------------------------------------------------------------------#
 MERCURY_CHECK_FOR_HEADERS( \
diff --git a/runtime/mercury_conf.h.in b/runtime/mercury_conf.h.in
index e43b4dc7f..9bdf79a52 100644
--- a/runtime/mercury_conf.h.in
+++ b/runtime/mercury_conf.h.in
@@ -245,6 +245,9 @@
 **	MR_HAVE_SYMLINK		we have the symlink function.
 **	MR_HAVE_READLINK	we have the readlink function.
 **	MR_HAVE_GETTIMEOFDAY	we have the gettimeofday function.
+**	MR_HAVE_SETENV		we have the setenv() function.
+**	MR_HAVE_PUTENV		we have the putenv() function.
+**	MR_HAVE__PUTENV		we have the _putenv() function.
 */
 #undef	MR_HAVE_GETPID
 #undef	MR_HAVE_SETPGID
@@ -301,6 +304,9 @@
 #undef	MR_HAVE_SYMLINK
 #undef	MR_HAVE_READLINK
 #undef	MR_HAVE_GETTIMEOFDAY
+#undef	MR_HAVE_SETENV
+#undef	MR_HAVE_PUTENV
+#undef	MR_HAVE__PUTENV
 
 /*
 ** We use mprotect() and signals to catch stack and heap overflows.
diff --git a/runtime/mercury_runtime_util.c b/runtime/mercury_runtime_util.c
index 869bfcb99..c9a5852d9 100644
--- a/runtime/mercury_runtime_util.c
+++ b/runtime/mercury_runtime_util.c
@@ -85,3 +85,36 @@ MR_checked_atexit(void (*func)(void))
         exit(EXIT_FAILURE);
     }
 }
+
+#if ! defined(MR_HAVE_PUTENV) && defined(MR_HAVE__PUTENV)
+  #define putenv _putenv
+#endif
+
+int
+MR_setenv(const char *name, const char *value, int overwrite)
+{
+#if defined(MR_HAVE_SETENV)
+    return setenv(name, value, overwrite);
+#elif defined(MR_HAVE_PUTENV) || defined(MR_HAVE__PUTENV)
+    char *env;
+    int length;
+
+    if (!overwrite && getenv(name) != NULL) {
+        return 0;
+    }
+
+    length = strlen(name) + strlen(value) + 2;
+    env = MR_NEW_ARRAY(char, length);
+
+    env[0] = '\0';
+    strcat(env, name);
+    strcat(env, "=");
+    strcat(env, value);
+
+    MR_free(env);
+    
+    return putenv(env);
+#else
+  #error "MR_setenv: unable to define"
+#endif
+}
diff --git a/runtime/mercury_runtime_util.h b/runtime/mercury_runtime_util.h
index 64cd6190a..d40fb2bd0 100644
--- a/runtime/mercury_runtime_util.h
+++ b/runtime/mercury_runtime_util.h
@@ -1,5 +1,5 @@
 /*
-** Copyright (C) 2001 The University of Melbourne.
+** Copyright (C) 2001,2006 The University of Melbourne.
 ** This file may only be copied under the terms of the GNU Library General
 ** Public License - see the file COPYING.LIB in the Mercury distribution.
 */
@@ -17,5 +17,6 @@ extern	FILE	*MR_checked_fopen(const char *filename, const char *message,
 			const char *mode);
 extern	void	MR_checked_fclose(FILE *file, const char *filename);
 extern	void	MR_checked_atexit(void (*func)(void));
+extern  int	MR_setenv(const char *name, const char *value, int overwrite);
 
 #endif	/* MERCURY_RUNTIME_UTIL_H */
diff --git a/runtime/mercury_trace_base.c b/runtime/mercury_trace_base.c
index 11f0c3681..446b304ec 100644
--- a/runtime/mercury_trace_base.c
+++ b/runtime/mercury_trace_base.c
@@ -415,9 +415,9 @@ MR_trace_record_label_exec_counts(void *dummy)
 
         old_options = getenv("MERCURY_OPTIONS");
         if (old_options != NULL) {
-            (void) setenv("MERCURY_OPTIONS", "", MR_TRUE);
+            (void) MR_setenv("MERCURY_OPTIONS", "", MR_TRUE);
             summary_status = system(cmd);
-            (void) setenv("MERCURY_OPTIONS", old_options, MR_TRUE);
+            (void) MR_setenv("MERCURY_OPTIONS", old_options, MR_TRUE);
         } else {
             summary_status = system(cmd);
         }
diff --git a/trace/Mmakefile b/trace/Mmakefile
index e5ff26ab4..6e4cdae43 100644
--- a/trace/Mmakefile
+++ b/trace/Mmakefile
@@ -153,7 +153,7 @@ ALLOW_MDBCOMP_PREFIX=no
 BISON		= bison
 BISON_OPTS	= -v
 FLEX		= flex
-FLEX_OPTS	= --8bit
+FLEX_OPTS	= -8
 
 MERCURY_DIR=..
 LINK_STDLIB_ONLY=yes
@@ -241,10 +241,10 @@ mercury_event_parser.c mercury_event_parser.h: mercury_event_parser.y
 
 mercury_event_scanner.c mercury_event_scanner.h: \
 		mercury_event_scanner.l mercury_event_parser.h
-	$(FLEX) $(FLEX_OPTS) -s -P mercury_event_ \
-		-o mercury_event_scanner.c \
-		--header-file=mercury_event_scanner.h \
+	$(FLEX) $(FLEX_OPTS) -s -Pmercury_event_ \
+		-omercury_event_scanner.c \
 		mercury_event_scanner.l
+	echo "extern int mercury_event_lex(void);" >  mercury_event_scanner.h
 
 RPATH_1=$(SHLIB_RPATH_OPT)$(FINAL_INSTALL_MERC_LIB_DIR)
 RPATH_2=$(SHLIB_RPATH_SEP)$(FINAL_INSTALL_MERC_GC_LIB_DIR)