diff --git a/lib/download.php b/lib/download.php
index 11a329b..079b3fb 100644
--- a/lib/download.php
+++ b/lib/download.php
@@ -6,7 +6,7 @@ include("settings.php");
 $file = realpath($docRoot.$iceRoot.str_replace("|","/",strClean($_GET['file'])));
 // If it doesn't exist, or doesn't start with the $docRoot, stop here
 if (!file_exists($file) || strpos(str_replace("\\","/",$file),$docRoot) !== 0) {
-	die("<script>alert('Sorry, that file doesn\'t appear to exist');</script>");
+	die("<script>top.ICEcoder.message('Sorry, that file doesn\'t appear to exist');</script>");
 }
 
 if (file_exists($file)) {
diff --git a/lib/file-control.php b/lib/file-control.php
index ba3e0dd..72167f2 100644
--- a/lib/file-control.php
+++ b/lib/file-control.php
@@ -59,7 +59,7 @@ for ($i=0; $i<count($allFiles); $i++) {
 		// Or a remote URL that doesn't start http
 		($_GET['action']=="getRemoteFile" && strpos($allFiles[$i],"http") !== 0)
 		) {
-		die("alert('Sorry! - problem with file requested');</script>");
+		die("top.ICEcoder.message('Sorry! - problem with file requested');</script>");
 	};
 }
 
@@ -97,7 +97,7 @@ if ($_GET['action']=="load") {
 			ftpStart();
 			// Show user warning if no good connection
 			if (!$ftpConn || !$ftpLogin) {
-				die('alert("Sorry, no FTP connection to '.$ftpHost.' for user '.$ftpUser.'");top.ICEcoder.serverMessage();top.ICEcoder.serverQueue("del",0);</script>');
+				die('top.ICEcoder.message("Sorry, no FTP connection to '.$ftpHost.' for user '.$ftpUser.'");top.ICEcoder.serverMessage();top.ICEcoder.serverQueue("del",0);</script>');
 				exit;
 			}
 			// Get our file contents and close the FTP connection
diff --git a/lib/github.php b/lib/github.php
index 0424774..cef7963 100644
--- a/lib/github.php
+++ b/lib/github.php
@@ -192,7 +192,7 @@ if (!$demoMode && isset($_SESSION['loggedIn']) && $_SESSION['loggedIn'] && isset
 				$loadedFile = toUTF8noBOM(file_get_contents($file,false,$context),true);
 				echo '<textarea name="loadedFile'.$i.'" id="loadedFile'.$i.'" style="display: none">'.str_replace("</textarea>","<ICEcoder:/:textarea>",str_replace("&","&amp;",$loadedFile)).'</textarea><br><br>'.PHP_EOL.PHP_EOL;
 			} else {
-				die("<script>alert('Sorry, that file doesn\'t appear to exist');</script>");
+				die("<script>top.ICEcoder.message('Sorry, that file doesn\'t appear to exist');</script>");
 			}
 		}
 		?>
diff --git a/test/index.php b/test/index.php
index ee1cc8c..c5d92a3 100644
--- a/test/index.php
+++ b/test/index.php
@@ -243,7 +243,7 @@ test = {
 				setTimeout(function() {
 					ICEcoder.closeTab(1,false,true);
 					console.log('TEST COMPLETE!');
-					alert('Test Complete!\n\nRan '+s+' of '+total+' tests OK.\nSee console for more details.');
+					top.ICEcoder.message('Test Complete!\n\nRan '+s+' of '+total+' tests OK.\nSee console for more details.');
 				},200);
 			} else {
 				testResult("- FAIL",title);
@@ -276,7 +276,7 @@ function displayResults(successful) {
 
 function testStopped() {
 	unitTestResults.innerHTML += " - Test stopped";
-	alert("Test stopped, see console for details.");
+	top.ICEcoder.message("Test stopped, see console for details.");
 }
 </script>