diff --git a/packages/CLPBN/clpbn/bp/Parfactor.cpp b/packages/CLPBN/clpbn/bp/Parfactor.cpp
index 60e7c1648..8d49136b7 100644
--- a/packages/CLPBN/clpbn/bp/Parfactor.cpp
+++ b/packages/CLPBN/clpbn/bp/Parfactor.cpp
@@ -660,8 +660,8 @@ Parfactor::alignAndExponentiate (Parfactor* g1, Parfactor* g2)
   unsigned condCount2 = g2->constr()->getConditionalCount (Y_2);
   LogAware::pow (g1->params(), 1.0 / condCount2);
   LogAware::pow (g2->params(), 1.0 / condCount1);
-  // this must be done in the end or else X_1 and X_2 
-  // will refer the old log var names in the code above
+  // the alignment should be done in the end or else X_1 and X_2 
+  // will refer to the old log var names on the code above
   align (g1, X_1, g2, X_2);
 }
 
@@ -673,24 +673,39 @@ Parfactor::align (
     Parfactor* g2, const LogVars& alignLvs2)
 {
   LogVar freeLogVar = 0;
-  Substitution theta1;
-  Substitution theta2;
+  Substitution theta1, theta2;
+  for (unsigned i = 0; i < alignLvs1.size(); i++) {
+    bool b1 = theta1.containsReplacementFor (alignLvs1[i]); 
+    bool b2 = theta2.containsReplacementFor (alignLvs2[i]);
+    // handle this type of situation:
+    // g1 = p(X), q(X) ; X in {x1} 
+    // g2 = p(X), q(Y) ; X in {x1}, Y in {x1}
+    if (b1 == false && b2 == false) {
+      theta1.add (alignLvs1[i], freeLogVar);
+      theta2.add (alignLvs2[i], freeLogVar);
+      ++ freeLogVar;
+    } else if (b1 == false && b2) {
+      theta1.add (alignLvs1[i], theta2.newNameFor (alignLvs2[i]));
+    } else if (b1 && b2 == false) {
+      theta2.add (alignLvs2[i], theta1.newNameFor (alignLvs1[i]));
+    }
+  }
   const LogVarSet& allLvs1 = g1->logVarSet();
   for (unsigned i = 0; i < allLvs1.size(); i++) {
-    theta1.add (allLvs1[i], freeLogVar);
-    ++ freeLogVar;
+    if (theta1.containsReplacementFor (allLvs1[i]) == false) {
+      theta1.add (allLvs1[i], freeLogVar);
+      ++ freeLogVar;
+    }
   }
-
   const LogVarSet& allLvs2 = g2->logVarSet();
   for (unsigned i = 0; i < allLvs2.size(); i++) {
-    theta2.add (allLvs2[i], freeLogVar);
-    ++ freeLogVar;
-  }
-
-  assert (alignLvs1.size() == alignLvs2.size());
-  for (unsigned i = 0; i < alignLvs1.size(); i++) {
-    theta1.rename (alignLvs1[i], theta2.newNameFor (alignLvs2[i]));
+    if (theta2.containsReplacementFor (allLvs2[i]) == false) {
+      theta2.add (allLvs2[i], freeLogVar);
+      ++ freeLogVar;
+    }
   }
+  // cout << "theta1: " << theta1 << endl;
+  // cout << "theta2: " << theta2 << endl;
   g1->applySubstitution (theta1);
   g2->applySubstitution (theta2);
 }