Index: /trunk/ppStack/src/ppStackMatch.c
===================================================================
--- /trunk/ppStack/src/ppStackMatch.c	(revision 35867)
+++ /trunk/ppStack/src/ppStackMatch.c	(revision 35868)
@@ -467,9 +467,15 @@
 		sum += kernels->rms;
                 num++;
-		//		psLogMsg("ppStack", PS_LOG_INFO, "KERNMATCHDUMP %d %d %g %g %g\n",
-		//			 index,num,kernels->mean,kernels->rms,sum);
+		//				psLogMsg("ppStack", PS_LOG_INFO, "KERNMATCHDUMP %d %d %g %g %g %g\n",
+		//					 index,num,kernels->mean,kernels->rms,sum,psImageCovarianceFactor(readout->covariance));
             }
             psFree(iter);
-            options->matchChi2->data.F32[index] = sum / (psImageCovarianceFactor(readout->covariance) * num);
+
+	    // Apply the covariance factor to the chi^2 value
+	    double covar_factor = 1.0;
+	    if (type != PM_SUBTRACTION_KERNEL_SIMPLE) { // Except if we're using simple kernels.
+	      covar_factor = psImageCovarianceFactor(readout->covariance);
+	    }
+            options->matchChi2->data.F32[index] = sum / (covar_factor * num);
 
         }
Index: /trunk/ppStack/src/ppStackUpdateHeader.c
===================================================================
--- /trunk/ppStack/src/ppStackUpdateHeader.c	(revision 35867)
+++ /trunk/ppStack/src/ppStackUpdateHeader.c	(revision 35868)
@@ -98,4 +98,7 @@
 
 	float value = options->norm ? pow(10.0, -0.4*options->norm->data.F32[i]) : NAN;
+	if ((options->inputMask)&&(options->inputMask->data.PS_TYPE_VECTOR_MASK_DATA[i])) {
+	  value = 0.0; // If this is NAN, then it's recorded in the header as a character string instead of a float.
+	}
 	snprintf (field, 64, "SCL_%04d", i);
 	psMetadataAddF32(hdu->header, PS_LIST_TAIL, field, PS_META_REPLACE, "input image scale factor", value);
@@ -132,4 +135,5 @@
 	expROhdu->header = psMetadataAlloc();
       }
+
       expRO->parent->parent->parent->hdu->header = psMetadataCopy(expRO->parent->parent->parent->hdu->header,
 								  outRO->parent->parent->parent->hdu->header);