ehm...

std/js/JQuery.hx

@@ -345,7 +345,7 @@ extern class JQuery implements ArrayAccess<Dom.HtmlDom> {
 	}
 
 	private static function __init__() : Void untyped {
-		#if !embedJs
+		#if embedJs
 		if( untyped __js__("typeof($) == 'undefined'") )
 			haxe.macro.Tools.includeFile("js/jquery-latest.min.js");
 		#end

std/js/SWFObject.hx

@@ -11,7 +11,7 @@ extern class SWFObject {
 	function setAttribute( id : String, value : String ) : Void;
 
 	private static function __init__() : Void untyped {
-		#if !embedJs
+		#if embedJs
 		haxe.macro.Tools.includeFile("js/swfobject-1.5.js");
 		#end
 		js.SWFObject = deconcept.SWFObject;