Overriding TinyMCE buttons – Justify button shortcodes not working

Because you are using button references to version 3 of TinyMCE. Beginning in WordPress version 3.9; TinyMCE 4 is being used.

Check this page, then click the “View Source” tab to see the new button names.

Working from your array above:

TinyMCE 3        TinyMCE 4
justifyleft   => alignleft
justifycenter => aligncenter
justifyright  => alignright

As far as I know, the separator button has been removed from WordPress core. I believe they removed the css rules which allowed the separator previously. This WordPress Trac Ticket may explain more.