I have the following code, (edit:) now without aligned.
\documentclass{beamer}
\mode<presentation> { \setbeamercovered{transparent} }
\begin{document}
\begin{frame}
\[
\begin{cases}
%\begin{aligned}
v(t,x) &= g(t,x), \\
\pause
u(x) &= f(x) %& (x\in\mathbb R)
%\end{aligned}
\end{cases}
\]
\end{frame}
\end{document}
(In the first version of the question, nothing was commented out.)
It compiles nicely, but everything except "u(x)" already shows up on the first slide if I use beamer.cls v 1.70 2007/03/11 18:50:44. On another computer at work we have an older version installed, namely v 1.55 2004/10/11 16:09:50; there everything works as expected: On the first slide, the full second line is shown in transparent style.
The same happens if I use plain TeX's \halign, so cases is not the culprit. Moreover, if I don't use \setbeamercovered{transparent}, then everything works as expected. In other words, \pause doesn't work together with \setbeamercovered{transparent} and \halign.
Is this a bug in beamer introduced between versions 1.55 and 1.70? (If yes, then I'm surprised since it'd regard it quite a serious one.) Does anyone know a workaround that doesn't involve as much markup as Matthew's answer to my original question?

\listfileson both systems and report any other differences in addition tobeamer. (Also, this might be best as a bug report forbeamer.) – Joseph Wright Dec 01 '10 at 18:05amssymbandamsfonts. – Hendrik Vogt Dec 01 '10 at 19:45pdftex.def. On my old installation I have the version2002/06/19 v0.03k, and with this it works as expected! I haven't yet the slightest clue why this is so. – Hendrik Vogt Sep 13 '12 at 19:26aligndoes wicked things,\pauseworks amazingly well insidealignwith my oldpdftex.def. Do you know by any chance where I can find all the other old versions? So that I can look for the last "working" version?) – Hendrik Vogt Sep 13 '12 at 20:020.03r, and the last "working" version is0.03t. From0.04I get the observed buggy behaviour. – Hendrik Vogt Sep 13 '12 at 20:24