If amsmath is loaded after zref-perpage, zref-perpage will not reset counters in each page. What should be done to fix this except changing the loading order:
\documentclass{article}
\usepackage{zref-perpage}
\zmakeperpage{footnote}
\usepackage{amsmath}
\begin{document}
This is a test \footnote{test}
\newpage
This is another test \footnote{test}
\end{document}