diff -up ./src/org/eclipse/linuxtools/cdt/autotools/AutotoolsScannerInfo.java.fix ./src/org/eclipse/linuxtools/cdt/autotools/AutotoolsScannerInfo.java
--- ./src/org/eclipse/linuxtools/cdt/autotools/AutotoolsScannerInfo.java.fix	2009-06-15 15:41:38.000000000 -0400
+++ ./src/org/eclipse/linuxtools/cdt/autotools/AutotoolsScannerInfo.java	2009-06-15 15:42:10.000000000 -0400
@@ -105,8 +105,8 @@ public class AutotoolsScannerInfo implem
 					String id = options[i].getId();
 					if (id.indexOf("builddir") > 0) { // $NON-NLS-1$
 						runPath = makefile.getProject().getLocation().append(value.trim());
+						done = true;
 					}
-					done = true;
 				}
 			} catch (BuildException e) {
 				// do nothing