I don't know if this is common knowledge, but Atmel have released an updated version of avr32program.
$ avr32program -V avr32program 3.0.4 Copyright (C) 2006-2008 Atmel Corporation
Not sure what changes there are though !!
Ah, I see it's part of the latest Atmel toolchain ...
GNU Toolchain/Release Notes 2.0.3 Product Name AVR32 GNU Toolchain Release Version 2.0.3 Release Date 2008-04-04