The batch file could be changed to use the pfi directly, but I have Windows 7 and it kept complaining about the wrong version of Java. So I installed a 32 bit version of Java ("C:\Program Files (x86)\Java\jre1.5.0_22\bin\java.exe") and run it from the jar ("C:\Program Files (x86)\Adobe\Adobe Flash CS5\PFI\lib\pfi.jar"). If you have Flash CS5, this will let you compile an ipa file without tying up Flash.
I'm using the german iPhone template, but I was having the same issue regarding the 64 bit version of java. I managed to fix the problem by editing the pfi.bat file inside the flex directory to load the 32 bit version explicitly:
So I replaced:
@java -Xms256m -Xmx1024m -jar "%~dp0\..\lib\pfi.jar" %*
@"C:\Program Files (x86)\Java\jre6\bin\java" -Xms256m -Xmx1024m -jar "%~dp0\..\lib\pfi.jar" %*
With the full path specified the 32 bit version is loaded explictly and the batch file/packager works a charm.
Hope that helps!