InputPayManaBase will execute input queue unlock from the same thread that was used to activate mana ability. No showMessage() will be called.

src/main/java/forge/control/input/InputPayManaBase.java

@@ -185,7 +185,10 @@ public abstract class InputPayManaBase extends InputSyncronizedBase implements I
             public void run() {
                 HumanPlay.playSpellAbility(chosen.getActivatingPlayer(), chosen);
                 onManaAbilityPlayed(chosen);
-                FThreads.invokeInEdtLater(new Runnable() { @Override public void run() { showMessage(); } });
+                if( isAlredyPaid() ) {
+                    done();
+                    stopNonEdt();
+                }
             }
         };
         game.getInputQueue().invokeGameAction(proc);
@@ -238,11 +241,11 @@ public abstract class InputPayManaBase extends InputSyncronizedBase implements I
             player.getZone(ZoneType.Battlefield).updateObservers();
     }
     
-    protected final void checkIfAlredyPaid() {
+    protected boolean isAlredyPaid() {
         if (manaCost.isPaid()) {
             bPaid = true;
-            done();
         }
+        return bPaid;
     }
     
     protected void onManaAbilityPaid() {} // some inputs overload it

src/main/java/forge/control/input/InputPayManaExecuteCommands.java

@@ -85,6 +85,7 @@ public class InputPayManaExecuteCommands extends InputPayManaBase {
 
             if (this.manaCost.isPaid()) {
                 this.done();
+                this.stop();
             } else {
                 this.showMessage();
             }
@@ -98,7 +99,6 @@ public class InputPayManaExecuteCommands extends InputPayManaBase {
         }
         player.getManaPool().clearManaPaid(this.saPaidFor, false);
         bPaid = true;
-        this.stop();
     }
 
     /** {@inheritDoc} */
@@ -126,7 +126,10 @@ public class InputPayManaExecuteCommands extends InputPayManaBase {
             msg.append("\n(Click on your life total to pay life for phyrexian mana.)");
         }
 
+        if( isAlredyPaid() ) {
+            done();
+            stop();
+        } else
             showMessage(msg.toString());
-        checkIfAlredyPaid();
     }
 }

src/main/java/forge/control/input/InputPayManaOfCostPayment.java

@@ -40,7 +40,6 @@ public class InputPayManaOfCostPayment extends InputPayManaBase {
         // any mana tapabilities can't be used in payment as well as being tapped for convoke)
 
         handleConvokedCards(false);
-        stop();
     }
     
     @Override
@@ -67,7 +66,10 @@ public class InputPayManaOfCostPayment extends InputPayManaBase {
             msg.append("\n(Click on your life total to pay life for phyrexian mana.)");
         }
 
+        if( isAlredyPaid() ) {
+            done();
+            stop();
+        } else
             showMessage(msg.toString());
-        checkIfAlredyPaid();
     }
 }

src/main/java/forge/control/input/InputPayManaSimple.java

@@ -89,8 +89,6 @@ public class InputPayManaSimple extends InputPayManaBase {
 
             handleConvokedCards(false);
         }
-
-        stop();
     }
 
     /** {@inheritDoc} */
@@ -127,6 +125,7 @@ public class InputPayManaSimple extends InputPayManaBase {
         if (this.manaCost.isPaid() && !new ManaCostBeingPaid(this.originalManaCost).isPaid()) {
             this.originalCard.setSunburstValue(this.manaCost.getSunburst());
             this.done();
+            this.stop();
         }
 
     }

src/main/java/forge/control/input/InputPayManaX.java

@@ -102,6 +102,7 @@ public class InputPayManaX extends InputPayManaBase {
     @Override
     protected final void onOk() {
         done();
+        this.stop();
     }
 
     @Override
@@ -116,6 +117,5 @@ public class InputPayManaX extends InputPayManaBase {
         card.setXManaCostPaid(this.xPaid);
         card.setColorsPaid(this.colorsPaid);
         card.setSunburstValue(ColorSet.fromMask(this.colorsPaid).countColors());
-        this.stop();
     }
 }

src/main/java/forge/control/input/InputSyncronizedBase.java

@@ -28,6 +28,7 @@ public abstract class InputSyncronizedBase extends InputBase implements InputSyn
     
     
     protected final void stop() {
+        
         setFinished();
         FThreads.invokeInNewThread(new Runnable() {
             @Override
@@ -39,6 +40,18 @@ public abstract class InputSyncronizedBase extends InputBase implements InputSyn
         });
     }
     
+    // This version does not need to be ran from EDT.
+    protected final void stopNonEdt() {
+        FThreads.assertExecutedByEdt(false);
+        
+        // ensure no clicks from EDT will be accepted
+        FThreads.invokeInEdtLater(new Runnable() { @Override public void run() { setFinished(); } }); 
+        
+        // this will update input proxy, so there might be anything happening in the thread 
+        getQueue().removeInput(InputSyncronizedBase.this);
+        cdlDone.countDown();
+    }
+
     @Override
     public final void selectButtonCancel() {
         if( isFinished() ) return;