I am using beamer and smashoperator as follows: \documentclass[xcolor={rgb}]{beamer} \setbeamercovered{transparent} \beamertemplatenavigationsymbolsempty \setbeamersize{text margin left=10mm,text margin right=5mm} \setbeamertemplate{frametitle}[default][center] \usepackage{mathtools} \usepackage{bm} \newcommand{\var}[1]{\operatorname{var}{#1}} \newcommand{\E}{\mathbb{E}} \newcommand{\norm}[1]{\left\lVert#1\right\rVert} \begin{document} \begin{frame}[t] \begin{align*} \onslide<2->{&= \E\Bigl( g(a)^2 \smashoperator{\sum_{j\in[n]\backslash\{a\}}} f^2_j Y^2_j + \smashoperator{\sum_{\substack{j\in[n]\setminus\{a\}\\i\ne j}}} f_i f_j g(i) g(j) Y_i B_j\Bigr) -{}\\} \onslide<2->{&\qquad\qquad\qquad\qquad \Bigl(\smashoperator{\sum_{j\in[n]\backslash\{a\}}} f_j \mathbb{E}[g(a)g(j)Y_j]\Bigr)^2\\[\jot]} \onslide<3->{&= \sum_{j\in[n]\backslash\{a\}} \frac{f^2_j}{k} + 0 - 0\\[\jot]} \end{align*} \end{frame} \end{document} However this gives an odd result. [![enter image description here][1]][1] Is there any way to fix this? [1]: https://i.stack.imgur.com/iGhkL.png

I think you have discovered a bug, and you got already an excellent workaround. However, here is another way to obtain this result, which might be even a bit shorter. More importantly, the fact that this method works may allow us to come up with educated guesses on what's going on. All you need to do is to ["repair" the `\pause` command](https://topanswers.xyz/tex?q=1126#a1350). I do not want to repeat all information from the linked post, but the `align` and so on environments "run" the code twice, one time in a "measuring" phase and then "for real". By suppressing the measuring phase in `\pause`, your issue gets solved, too. This seems to suggest that the `\smashoperator` uses the "wrong" boxes in the subscripts of the sum. ``` \documentclass[xcolor={rgb}]{beamer} \setbeamercovered{transparent} \beamertemplatenavigationsymbolsempty \setbeamersize{text margin left=10mm,text margin right=5mm} \setbeamertemplate{frametitle}[default][center] \usepackage{mathtools} \usepackage{bm} \newcommand{\var}[1]{\operatorname{var}{#1}} \newcommand{\E}{\mathbb{E}} \newcommand{\norm}[1]{\left\lVert#1\right\rVert} \makeatletter \renewrobustcmd{\beamer@@pause}[1][]{% \unless\ifmeasuring@% \ifblank{#1}% {\stepcounter{beamerpauses}}% {\setcounter{beamerpauses}{#1}}% \onslide<\value{beamerpauses}->\relax% \fi } \makeatother \begin{document} \begin{frame}[t] \pause \begin{align*} &= \E\Bigl( g(a)^2 \smashoperator{\sum_{j\in[n]\backslash\{a\}}} f^2_j Y^2_j + \smashoperator{\sum_{\substack{j\in[n]\setminus\{a\}\\i\ne j}}} f_i f_j g(i) g(j) Y_i B_j\Bigr) -{}\\ &\qquad\qquad\qquad\qquad \Bigl(\smashoperator{\sum_{j\in[n]\backslash\{a\}}} f_j \mathbb{E}[g(a)g(j)Y_j]\Bigr)^2\\[\jot] \pause &= \sum_{j\in[n]\backslash\{a\}} \frac{f^2_j}{k} + 0 - 0\\[\jot] \end{align*} \end{frame} \end{document} ``` ![ani.gif](/image?hash=99ceb90a047f4c8077f34fb08a0323cf2ecd69272353fb6e5ff4ac516ccbb5f5)

As a workaround, you can add the colour yourself: ``` \documentclass[xcolor={rgb}]{beamer} \setbeamercovered{transparent} \beamertemplatenavigationsymbolsempty \setbeamersize{text margin left=10mm,text margin right=5mm} \setbeamertemplate{frametitle}[default][center] \usepackage{mathtools} \usepackage{bm} \newcommand{\var}[1]{\operatorname{var}{#1}} \newcommand{\E}{\mathbb{E}} \newcommand{\norm}[1]{\left\lVert#1\right\rVert} \begin{document} \begin{frame}[t] \begin{align*} \onslide<1->{&= \E\Bigl( g(a)^2 \smashoperator{\sum_{j\in[n]\backslash\{a\}}} f^2_j Y^2_j + \smashoperator{\sum_{\substack{j\in[n]\setminus\{a\}\\i\ne j}}} f_i f_j g(i) g(j) Y_i B_j\Bigr) -{}\\} \onslide<2->{&\qquad\qquad\qquad\qquad \Bigl(\smashoperator{\sum_{\alt<2->{}{\color{.!85!bg}}j\in[n]\backslash\{a\}}} f_j \mathbb{E}[g(a)g(j)Y_j]\Bigr)^2\\[\jot]} \onslide<3->{&= \sum_{j\in[n]\backslash\{a\}} \frac{f^2_j}{k} + 0 - 0\\[\jot]} \end{align*} \end{frame} \end{document} ``` ![document.gif](/image?hash=7b81963306e1ce7f1566d927d33018d6c9342180252ac7d754fe0ab65455e443)