Beamer boxing a formula after a pause

First: you don't use align properly. You have to write "c=d" inside the environementalign, and "glue" the two equations with an &.

Second: you have to precisely align "d" correspondig to the differences between the width of d and boxed{d}.

There are two solutions (assuming that the frame is center-aligned); both of the should work, but shomehow the second is better.

documentclass{beamer}

% For both solutions
usepackage{calc}

% Just for the second solution
newlength{firslength}
settowidth{firslength}{boxed{d}}
newlength{secondlength}
settowidth{secondlength}{d}

begin{document}

begin{frame}

% First solution
begin{align*}
a=&b+only<1-2>{hspace*{(widthof{boxed{d}}-widthof{d})/2}chspace*{(widthof{boxed{d}}-widthof{d})/2}}%
only<3>{hspace*{(widthof{boxed{d}}-widthof{d})/2}dhspace*{(widthof{boxed{d}}-widthof{d})/2}}%
only<4>{boxed{d}}%
uncover<2->{c=&d}%
end{align*}

% Second solution
begin{align*}
a=&b+only<1-2>{hspace*{dimexpr(firslength-secondlength)/2}chspace{dimexpr(firslength-secondlength)/2}}%
only<3>{hspace*{dimexpr(firslength-secondlength)/2}dhspace{dimexpr(firslength-secondlength)/2}}%
only<4>{boxed{d}}%
uncover<2->{c=&d}%
end{align*}

end{frame}

end{document}