How to prevent Autocomplete Caching?
Since, there is no proper way, I opted for hack (or work around) to get this working. As already mentioned by @Clive, removing/disabling caching mechanism would require more work. This solution just skips the caching part.

Step1: Copy the entire misc/autocomplete.js to your module js scripts directory.

Step2: Comment or remove the following line from the copied file

// See if this key has been searched for before.
  //if (this.cache[searchString]) {
      // We dont want some things to be cached
    //return this.owner.found(this.cache[searchString]);
  //}


Step3: Implement hook_js_alter to override it to specific pages you like.

/**
 * Implements hook_js_alter
 * @param array $javascript
 */
function MYMODULE_js_alter(&amp;$javascript) {
  if (arg(0) == 'MYPAGE') {
    $javascript['misc/autocomplete.js']['data'] = drupal_get_path('module', 'MYMODULE') . '/js/autocomplete.js';
  } 
}