Index: /issm/trunk-jpl/etc/environment.sh
===================================================================
--- /issm/trunk-jpl/etc/environment.sh	(revision 11915)
+++ /issm/trunk-jpl/etc/environment.sh	(revision 11916)
@@ -1,6 +1,12 @@
 #ISSM_TIER and ISSM_ARCH should have been defined already in your shell settings file (.bashrc, .cshrc, etc ...)
+
+#Windows compilers: 
+if [[ "$ISSM_ARCH" == "cygwin-intel" ]]; then
+	source $ISSM_TIER/externalpackages/windows/windows_environment.sh
+fi
+
 source $ISSM_TIER/etc/environment_variables.sh
 
-#Do we have any command line arguments? (such as MATLAB_DIR=otherdirthandefault), source them before exporting the variables 
+#Do we have any command line arguments? (such as MATLAB_DIR=otherdirthandefault), source them after exporting the variables
 #to environment.
 for i in $@
@@ -8,11 +14,4 @@
 	eval $i
 done
-
-#Windows compilers: 
-if [[ "$ISSM_ARCH" == "cygwin-intel" ]]; then
-	source $ISSM_TIER/externalpackages/windows/windows_environment.sh
-fi
-
-source $ISSM_TIER/etc/environment_variables.sh
 
 #CRON utilities