Yes, CKEditor takes a very long time to load with uncompressed Javascript, and during the loading time it seems to have "disappeared." However in 20 seconds or so it should be back. Furthermore, if you have your browser cache turned on, it should only take this long the first time.
Unfortunately, that is the only way currently for custom BB-Code buttons to work until vBulletin posts a compressed version of the fix. If you have VaultWiki enabled, you can also avoid the button issue by hiding all the buttons from the editor using:
- in Lite, a plugin (I think you add to array $vault->misc['remove_tags']).
- in full, use the Wiki Code Manager