One problem seems to be that following Pololu's aforementioned guide, pg 15, step 5, tells me to select AVRISP as the Platform. Connecting in this mode, neither the Atmega128RFA1 or Atmega640 show up in the "Device and Signature Bytes" listing. I'm not sure what to say about this.
If instead I select STK500, these are both available. I can then try Read Signature. This worked for the Axon (Atmega640) but not for the Axon Mote.
This lead me to Section 8 of Pololu's manual (troubleshooting!). It notes:
If the target AVR is running at a voltage lower than 5 V, you may need to decrease the minimum allowed
target VDD setting using the configuration utility (Section 3.d). The default minimum allowed target VDD
setting is too high to allow the programmer to program at low voltages. Please note that you might need to
take additional special steps to safely program an AVR that is running off of a voltage below VUSB-0.5 V.
The configuration utility for this programmer is located at C:\Program Files (x86)\Pololu\USB AVR Programmer\pgm03a_config.exe or similar.
In the config utility's Target VDD Monitor section, I set the minimum allowed to 3264 mV (# is from measurements section). Clicked Refresh, then Apply, and then Disconnect or OK. Back in AVR Studio, Read Signature now works with the Mote.
From there it was straightforward with the instructions to put a new program on the Mote
(I also ended up reinstalling AVR Studio... which was a PITA itself - had to follow stuff in this thread
to get around a problem with the installer (both 4.18 and 4.19...) hanging)
(I also tried with WinXP SP2... I don't think the Pololu programmer is working, unfortunately, despite applying the USB patch, as in this thread
. I can't connect to the programmer in AVR Studio 4 on XP SP2.)