Hi Jon, yes it's an issue for UNOs of a certain vintage - ones that have a certain kind of bootloader that misreports the available space. It was covered briefly on the blog here (started with http://www.polargraph.co.uk/2012/06/polargraph-controller-v1-1-7/#comment-1636)

and I never really came up with a fix. I don't know if loading a precompiled hex file helps at all (http://www.polargraph.co.uk/2012/07/more-updating-firmware-without-using-arduino/ and http://www.polargraph.co.uk/2012/06/uploading-firmware-without-arduino/), and it might be worth a try, but it uses avrdude too, so I imagine it doesn't help.

The solution, such as it is, is to burn a newer bootloader onto the UNO.

good luck!
sn

Hi Jonpetersen, I realize this is a very very late response but maybe it will help someone else in a similar situation, I had the same problem, I found a very crude fix however it results in you loosing the ability to lift the pen with a servo but a small price to pay if you just want to mess around with a polargraph.

- Open the polargraph_server_a1 sketch in arduino IDE,
- delete the #include <Servo.h> line,
- Now delete all the associated servo code, easiest way to do this is to "compile" the sketch and delete all lines highlighted with errors.

This worked for me, but this is my first attempt at a polargraph so I have not played around enough to know if I screwed up more advanced features but the basic sketching still works fine.