diff --git a/build/org.eclipse.cdt.make.core/src/org/eclipse/cdt/make/core/MakeProjectNature.java b/build/org.eclipse.cdt.make.core/src/org/eclipse/cdt/make/core/MakeProjectNature.java
index 1e00511c1e2..a9586450b6c 100644
--- a/build/org.eclipse.cdt.make.core/src/org/eclipse/cdt/make/core/MakeProjectNature.java
+++ b/build/org.eclipse.cdt.make.core/src/org/eclipse/cdt/make/core/MakeProjectNature.java
@@ -64,7 +64,7 @@ public class MakeProjectNature implements IProjectNature {
 			newCommands[0] = newCommand;
 		} else {
 			for (int i = 0, max = oldCommands.length; i < max; i++) {
-				if (oldCommands[i] == oldCommand) {
+				if (oldCommands[i].getBuilderName().equals(oldCommand.getBuilderName())) {
 					oldCommands[i] = newCommand;
 					break;
 				}