tc@box:~$ grep layer .jwm*
.jwmrc-tray: <!-- Additional tray attributes: autohide, width, border, layer, layout -->
.jwmrc-tray: <Tray x="0" y="0" height="15" layer="3">
autohide versus layer are separate attributes.
Before you change jwm config I suggest you test with changing layer of your apps window, e.g. Layer -> Top