diff --git a/lib/ace/mode/clojure_highlight_rules.js b/lib/ace/mode/clojure_highlight_rules.js
index 91a744f9..d5e8ed88 100644
--- a/lib/ace/mode/clojure_highlight_rules.js
+++ b/lib/ace/mode/clojure_highlight_rules.js
@@ -138,9 +138,9 @@ var ClojureHighlightRules = function() {
                 token : "comment",
                 regex : ";.*$"
             }, {
-                    token : "comment", // multi line comment
-                    regex : "^\=begin$",
-                    next : "comment"
+                token : "comment", // multi line comment
+                regex : "^=begin$",
+                next : "comment"
             }, {
                 token : "keyword", //parens
                 regex : "[\\(|\\)]"
@@ -193,17 +193,17 @@ var ClojureHighlightRules = function() {
                 regex : '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]'
             }, {
                 token : "string", // symbol
-                regex : "[:](?:[a-zA-Z]|\d)+"
+                regex : "[:](?:[a-zA-Z]|\\d)+"
             }, {
-            token : "string.regexp", //Regular Expressions
-            regex : '/#"(?:\.|(\\\")|[^\""\n])*"/g'
+                token : "string.regexp", //Regular Expressions
+                regex : '/#"(?:\\.|(?:\\\")|[^\""\n])*"/g'
             }
-              
+
         ],
         "comment" : [
             {
                 token : "comment", // closing comment
-                regex : "^\=end$",
+                regex : "^=end$",
                 next : "start"
             }, {
                 token : "comment", // comment spanning whole line
diff --git a/lib/ace/mode/markdown_highlight_rules.js b/lib/ace/mode/markdown_highlight_rules.js
index 319284fc..554d464e 100644
--- a/lib/ace/mode/markdown_highlight_rules.js
+++ b/lib/ace/mode/markdown_highlight_rules.js
@@ -64,7 +64,7 @@ var MarkdownHighlightRules = function() {
             token : "empty_line",
             regex : '^$'
         }, { // code span `
-            token : "support.function",
+            token : ["support.function", "support.function", "support.function"],
             regex : "(`+)([^\\r]*?[^`])(\\1)"
         }, { // code block
             token : "support.function",
@@ -94,7 +94,7 @@ var MarkdownHighlightRules = function() {
             next  : "blockquote"
         }, { // reference
             token : ["text", "constant", "text", "url", "string", "text"],
-            regex : "^([ ]{0,3}\\[)([^\\]]+)(\\]:\\s*)([^ ]+)(\\s*(?:[\"][^\"]+[\"])?\\s*)$"
+            regex : "^([ ]{0,3}\\[)([^\\]]+)(\\]:\\s*)([^ ]+)(\\s*(?:[\"][^\"]+[\"])?(\\s*))$"
         }, { // link by reference
             token : ["text", "string", "text", "constant", "text"],
             regex : "(\\[)((?:[[^\\]]*\\]|[^\\[\\]])*)(\\][ ]?(?:\\n[ ]*)?\\[)(.*?)(\\])"
@@ -120,10 +120,10 @@ var MarkdownHighlightRules = function() {
             regex : "^\\s{0,3}(?:[*+-]|\\d+\\.)\\s+",
             next  : "listblock"
         }, { // strong ** __
-            token : "string",
+            token : ["string", "string", "string"],
             regex : "([*]{2}|[_]{2}(?=\\S))([^\\r]*?\\S[*_]*)(\\1)"
         }, { // emphasis * _
-            token : "string",
+            token : ["string", "string", "string"],
             regex : "([*]|[_](?=\\S))([^\\r]*?\\S[*_]*)(\\1)"
         }, { // 
             token : ["text", "url", "text"],
diff --git a/lib/ace/tokenizer.js b/lib/ace/tokenizer.js
index a471aa76..afd50b76 100644
--- a/lib/ace/tokenizer.js
+++ b/lib/ace/tokenizer.js
@@ -62,7 +62,7 @@ var Tokenizer = function(rules, flag) {
             });
             
             if (matchcount > 1 && state[i].token.length !== matchcount-1)
-                throw new Error("Matching groups and length of the token array don't match");
+                throw new Error("Matching groups and length of the token array don't match in rule #" + i + " of state " + key);
             
             mapping[matchTotal] = {
                 rule: i,