diff --git a/resources/MatlabInterface/@JEInterface/evaluateJE.m b/resources/MatlabInterface/@JEInterface/evaluateJE.m
deleted file mode 100644
index 0206afa3..00000000
--- a/resources/MatlabInterface/@JEInterface/evaluateJE.m
+++ /dev/null
@@ -1,11 +0,0 @@
-function v = evaluate(int)
-% Interface function for JavaEvA 2.
-% Will be called by the MatlabProblem to obtain the target function value
-% for a sample individual.
-
-x = int.mp.getCurrentDoubleArray;
-if (isempty(int.args))
-    int.mp.setResult(feval(int.f, x));
-else
-    int.mp.setResult(feval(int.f, x, int.args));
-end
diff --git a/resources/MatlabInterface/@JEInterface/isFinished.m b/resources/MatlabInterface/@JEInterface/isFinished.m
index f6163b82..2ebb4cdb 100644
--- a/resources/MatlabInterface/@JEInterface/isFinished.m
+++ b/resources/MatlabInterface/@JEInterface/isFinished.m
@@ -1,4 +1,5 @@
 function b = isFinished(int)
+% Deprecated: optimization now runs synchronously. 
 % Returns 1 if the optimization was finished, else 0
 
 b = int.finished;
diff --git a/resources/MatlabInterface/@JEInterface/runEvalLoopJE.m b/resources/MatlabInterface/@JEInterface/runEvalLoopJE.m
index ca4ae9c3..1fae3eaf 100644
--- a/resources/MatlabInterface/@JEInterface/runEvalLoopJE.m
+++ b/resources/MatlabInterface/@JEInterface/runEvalLoopJE.m
@@ -9,6 +9,7 @@ function int=runEvalLoopJE(int, optOrPostProc, optType, outputFilePrefix, steps,
 % when optimizing. nBest may be -1 to show all.
 
 global stopOptimization
+global JEMediator
 
 if ~isempty(int.mediator)
     int.mediator.quit
@@ -18,6 +19,7 @@ end
 % set up a mediator and inform JE
 int.mediator = javaeva.server.go.problems.MatlabEvalMediator;
 int.mp.setMediator(int.mediator);
+JEMediator=int.mediator;
 
 % start the JE thread
 if (optOrPostProc == 1)
@@ -34,7 +36,7 @@ end
 % stopOptimization is empty. if it is then it is not the toolbox calling
 % and we create an own button to stop it.
 if isempty(stopOptimization),
-    % create a cancel button box (only in the case that
+    % create a cancel button box (case without SBtoolbox)
     h=figure('Position',[100 600 250 80], 'MenuBar', 'none', 'Name', 'JavaEvA optimization running...', 'NumberTitle','off');
     uicontrol(h,'Style', 'pushbutton', 'String', 'Cancel', 'Position', [25 25 60 30], 'Callback', 'global stopOptimization; stopOptimization=1;');
     uicontrol(h,'Style', 'text', 'String', stopText, 'Position', [100 25 120 30]);
@@ -51,23 +53,34 @@ end
 stopOnce=1;
 
 % repeat the mediator thread and eval call until finished
-while (~int.mediator.isFinished())
-    int.mediator.run;
-    if (~int.mediator.isFinished())
-        x = int.mediator.getQuestion();
-        if (isempty(int.args))
-            res = feval(int.f, x);
-        else
-            res = feval(int.f, x, int.args);
-        end
-        int.mediator.setAnswer(res);
-        drawnow;
-        if ((stopOptimization==1) && (stopOnce==1))
-            disp('User interrupt requested ...');
-            stopOptimize(int);
-            stopOnce=0;
+try
+    while (~int.mediator.isFinished())
+        int.mediator.run;
+        if (~int.mediator.isFinished())
+            x = int.mediator.getQuestion();
+            if (isempty(int.args))
+                res = feval(int.f, x);
+            else
+                res = feval(int.f, x, int.args);
+            end
+            int.mediator.setAnswer(res);
+            drawnow;
+            if ((stopOptimization==1) && (stopOnce==1))
+                disp('User interrupt requested ...');
+                stopOptimize(int);
+                stopOnce=0;
+            end
         end
     end
+    clear global JEMediator;
+catch
+    disp('Error in evaluate!');
+    %int.mediator.quit; % just in case
+    %int.mediator='';
+    if (nontoolboxopt == 1)
+        if (ishandle(h)) , close(h); end
+        clear global stopOptimization
+    end
 end
 
 % write back results
@@ -81,6 +94,6 @@ int.mediator='';
 % and not from the toolboxes parameter estimation function (which has an
 % own stop button). we decide this by checking nontoolboxopt
 if nontoolboxopt == 1,
-    close(h);
+    if (ishandle(h)) , close(h); end
     clear global stopOptimization
-end
\ No newline at end of file
+end
diff --git a/resources/MatlabInterface/@JEInterface/stopOptimize.m b/resources/MatlabInterface/@JEInterface/stopOptimize.m
index b6cdcb87..5f99303b 100644
--- a/resources/MatlabInterface/@JEInterface/stopOptimize.m
+++ b/resources/MatlabInterface/@JEInterface/stopOptimize.m
@@ -1,9 +1,22 @@
-function int = stopOptimize(int)
-% Stop a running optimization
+function int = stopOptimize(int, varargin)
+% Stop a running optimization. 
+%   stopOptimize(JI [,'kill'])
+%       If 'kill' is given as second argument, the mediator thread is
+%       stopped, relevant if optimization was stopped using CTRL-C and the
+%       mediator is a running zombie.
 
+global JEMediator
+    
 %disp('in Stop!');
 int.mp.stopOptimize;
-%if (~isempty(int.mediator))
-%    int.mediator.quit; % just in case
-%    int.mediator='';
-%end
\ No newline at end of file
+
+if (nargin > 1) && (ischar(varargin{1}) && (strcmp(varargin{1},'kill')==1))
+    if (~isempty(JEMediator))
+        disp('killing mediator...');
+        JEMediator.quit; % just in case
+        JEMediator='';
+        clear global JEMediator;
+    else 
+        disp('no mediator to kill');
+    end
+end
\ No newline at end of file
diff --git a/src/javaeva/server/go/problems/MatlabEvalMediator.java b/src/javaeva/server/go/problems/MatlabEvalMediator.java
index 00f5f46b..ce67d2d3 100644
--- a/src/javaeva/server/go/problems/MatlabEvalMediator.java
+++ b/src/javaeva/server/go/problems/MatlabEvalMediator.java
@@ -1,5 +1,7 @@
 package javaeva.server.go.problems;
 
+import javaeva.gui.BeanInspector;
+
 /**
  * This implements a thread acting as a mediator between JavaEvA and Matlab. Thanks to the idea 
  * of Henning Schmidt!
@@ -26,7 +28,7 @@ public class MatlabEvalMediator implements Runnable {
 	volatile boolean fin = false;
 	volatile double[] question = null;
 	volatile double[] answer = null;
-	volatile boolean quit = false;
+	boolean quit = false;
 	volatile double[] optSolution = null;
 	volatile double[][] optSolSet = null;
 //	MatlabProblem mp = null;
@@ -44,17 +46,16 @@ public class MatlabEvalMediator implements Runnable {
 		question = x;
 		requesting = true;
 //		int k=0;
-//		mp.log("Requesting eval for " + BeanInspector.toString(x) + ", req state is " + requesting + "\n"); 
+//		System.out.println("Requesting eval for " + BeanInspector.toString(x) + ", req state is " + requesting + "\n"); 
 		while (requesting && !quit) {
 			// 	wait for matlab to answer the question
 			if (sleepTime > 0) try { Thread.sleep(sleepTime); } catch(Exception e) {};
-//			k++;
-//			if (k>100) {
+//			if ((k%100)==0) {
 //				System.out.println("waiting for matlab to answer...");
-//				k=0;
 //			}
+//			k++;
 		}
-//		mp.log("Requesting done \n");
+//		System.out.println("Requesting done \n");
 		// matlab is finished, answer is here
 		return getAnswer(); // return to JE with answer
 	}
@@ -67,13 +68,12 @@ public class MatlabEvalMediator implements Runnable {
 		while (!requesting && !isFinished() && !quit) {
 			// wait for JE to pose a question or finish all
 			if (sleepTime > 0) try { Thread.sleep(sleepTime); } catch(Exception e) {};
-//			k++;
-//			if (k>100) {
+//			if ((k%100)==0) {
 //				System.out.println("waiting for JE to ask...");
-//				k=0;
 //			}
+//			k++;
 		}
-//		mp.log("-- Request arrived in MP thread\n");
+//		System.out.println("-- Request arrived in MP thread\n");
 		// requesting is true, now finish and let Matlab work
 	}
 
@@ -81,6 +81,7 @@ public class MatlabEvalMediator implements Runnable {
 	 * Cancel waiting in any case.
 	 */
 	public void quit() {
+//		System.out.println("IN QUIT!");
 		quit = true;
 	}