TeXLive 2016: Standalone + pstricks not working

The issue is known and has been reported a the standalone bug tracker: https://bitbucket.org/martin_scharrer/standalone/issues/25/pagesize-special-clipping

Work arounds are:

\RequirePackage[nosetpagesize]{graphics}
\documentclass[pstricks]{standalone}
\begin{document}
\begin{pspicture}(0,0)(5,4)
\psline(0,0)(5,4)
\end{pspicture}


\begin{pspicture}(0,0)(3,5)
\psline(0,0)(3,5)
\end{pspicture}

\end{document}

or

\documentclass[pstricks]{standalone}
\makeatletter
\def\sa@papersize{%
    \global\let\sa@papersize\relax
    \global\sa@yoffset=\paperheight
\global \setbox \@begindvibox
    \vbox{%
    \special{papersize=\the\paperwidth,\the\paperheight}%
    \special{ps::%
        \@percentchar\@percentchar HiResBoundingBox: 0 0 \the\paperwidth\space\the\paperheight^^J%
    }%
\unvbox \@begindvibox }%
}
\makeatother
\begin{document}
\begin{pspicture}(0,0)(5,4)
\psline(0,0)(5,4)
\end{pspicture}


\begin{pspicture}(0,0)(3,5)
\psline(0,0)(3,5)
\end{pspicture}

\end{document}

Use the option preview as follows and you will get the expected result.

\documentclass[pstricks,preview]{standalone}
\begin{document}
\begin{pspicture}(0,0)(5,4)
\psline(0,0)(5,4)
\end{pspicture}
\end{document}