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align gets executed twice and you need to make \pause keep out of the way of the first run:
\documentclass[usenames, dvipsnames]{beamer}
\usepackage{amsmath, amssymb, amsthm, mathtools, commath, array, tcolorbox, cancel, caption, subcaption, graphicx, multicol,beamerthemesplit,stmaryrd,comment, ...