Admin menu disappearing
Here's a checklist of things to look at:


Drupal simply concatenates files during aggregation. Malformed scripts may cause the entire thing to blow up. Disable aggregation first to see the code in plain so it's easier to debug. 
Aggregation can also lead to some weird issues together with caching. Ensure that you've refreshed the cache for both Drupal, browser and any external file systems (i.e. S3) to ensure that you're working with updated code and content.
Malformed CSS, believe it or not, can also cause aggregation to blow up. Chrome does not show any error of this happening. However, Firefox prints a warning if it does. Debug in Firefox to see some errors not shown by Chrome.
If you're using S3 for storage, ensure that all of your resources are present. Sometimes, the file may not be accessible from S3, fail to upload to S3, or just be missing (i.e. deleted accidentally).
You already mentioned disabling admin menu caching. That has solved this problem for me in two projects.
Clear all caches (drush cc all). Always worked. :D