It's not enough for JPF itself to be portable :-) the scripts that make it work should also be portable to the widest range of UNIX/POSIX systems, not just to Linux.
Heres's a patch for the two most important files; it should be applied and it should be propagated to the other scripts in bin and build-tools/bin.
--- build-tools/bin/ant (revision 250)
+++ build-tools/bin/ant (working copy)
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/sh
#
# run ant with libs from the jpf-build-tools module
#
Index: bin/jpf
===================================================================
--- bin/jpf (revision 250)
+++ bin/jpf (working copy)
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/sh
#
# unix shell script to run jpf
#
ian:12$