GUI Texture not responding to OnMouseEnter

Can you post a screenshot? I am not sure how many gui element you have right now (i think there are 1 pause and 1 resume), and what gameObject you are attaching this script to? (empty, guiTexture, guiText or something else)

Answer to side question

Answered question in UnityAnswers : Continueing music after un-pausing

Edit (3rd Rev)

In Unity's documentation on OnMouseOver, your overwritten version of OnMouseOver() is called every time your mouse is over the GUIElement or Collider this script is attached to. However, in your case, you attach it to the camera (which is neither GUIElement or Collider).

In your question, you said that you combined and modify 2 scripts, so I am quite sure that all the OnMouse function are from 1 script. What you should do now is to make it 2 script again ( I throw in a few lines to allow communication between 2 scripts ).

Proposed Solution

Pause Script (Attach to camera or empty object)

 #pragma strict
   
 var pause : boolean = false;
 var clickTexture : ClickTexture[];
 private var allAudioSources : AudioSource[];
  
 function Awake() 
 { 
     EnableClick( false );
     
     for( var i : int = 0; i < clickTexture.Length; ++i ) 
       clickTexture[i].pauseScript = this;
 
     allAudioSources = FindObjectsOfType(AudioSource) as AudioSource[];
 }
  
  function PauseAllAudio() 
 {
     for(var audioS : AudioSource in allAudioSources) { audioS.Pause(); }
 }
  
 function ResumeAllAudio() 
 {
     //ResumeAllAudio is not fixed
     for(var audioS : AudioSource in allAudioSources) { audioS.Play(); }
 }
  
  
 function Update()
 {
      if(Input.GetKeyUp(KeyCode.Escape)) 
      {
         //Super lazy one-liner
         pause = !pause; 
 
         if(pause == true) 
         {
           Time.timeScale = 0.0; 
           EnableClick( true );        
           PauseAllAudio();
         }
         else 
         {
           Time.timeScale = 1.0;
           EnableClick( false );    
           ResumeAllAudio();
         }
      } 
 }
 
 function RunOption( str : String ) {
    if( str == "quit" ) {
        Application.LoadLevel("AliensMainMenu");
    }
    else if( str == "resume" ) {
       Time.timeScale = 1.0;
       EnableClick( false );    
       ResumeAllAudio();
    }
 }
 
 function EnableClick( b : boolean ) {
    for( var i : int = 0; i < clickTexture.Length; ++i ) 
        clickTexture[i].Show(b);
 }

ClickTexture Script (Attach to GUITextre/GUIText)

 var pauseScript : Pause;
 var optionString : String;
 
 function OnMouseEnter()
 {
        //change text color
        guiTexture.color = Color.red;
 }
  
 function OnMouseExit()
 {
  
      //change text color
     guiTexture.color = Color.white;
 }
  
 function OnMouseUp()
 {
     pauseScript.RunOption( optionString );
 }

 function Show( b : boolean ) {
     this.enabled = b;
 
     if( guiTexture ) {
         guiTexture.enabled = b;
     }
 
     if( guiText ) {
         guiText.enabled = b;
     }
 }