I think it was because of Elizabeth
Earlier in the movie when Beckett and Sparrow were making a deal of their own in the movie, Beckett asks what will happen to Elizabeth, to which Jack responds by asking why he's interested in her. Despite everything he had done to her, he still believed he would have her as his own, since he believes he can have everything as long as he works for it and kills the right people at the right time.
When the Dutchman resurfaces though, Beckett finds out that Will is its captain, since Elizabeth quickly realized the same thing even though she was on a completely different ship, like Beckett. Since Will is the captain of the Dutchman, by default making him immortal, he also is now outside of Beckett's control unlike Davy Jones. Beckett also knows very well that Elizabeth and Will are in love, and that Will is immortal now, meaning that Beckett has now lost control over the Dutchman, which he thought was still under his control when it resurfaces, and control over Elizabeth, who he wanted to be with.
As minor as those things sound, the fact that Beckett finally cannot get something he has wanted shakes him to his core, since he has always gotten what he wanted no matter what. While he could have shaken off this shock sooner or later, it came at the absolute worst possible time when two very powerful ships were bearing down on him. He froze up, and because every decision runs through him first, the order could not be given when it could have easily been given, and so Beckett and his ship were obliterated.