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.
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