I copied a .cvf, .grass, .foliage, and .octree files to a rackspace server, ran chunky -render .cvf. The .cvf specified to render a 1600x800 image. After the first dump on the server, the .cvf had been rewritten to canvas width and height = 400, and the output image was 400x400 pixels.
(I would look into this myself but I have some 'real work' I need to get to, hence trying to offload my chunky renders to Rackspace ;P)
Hmm, odd. I have a render running right now in headless on a server and it's managed to keep the original resolution.
I've reproduced using the latest version checked out from GitHub (commit 264caf3)
Commands to reproduce: http://robert.nuke24.net:8080/~stevens/share/2013/Chunky-canvas-size-reset-log.txt
Data files: http://robert.nuke24.net:8080/~stevens/share/2013/CarpIntersectionTower1ae-test-2013.03.21.zip
The dumped images and the speed at which they are rendered also confirm that the canvas size in the original .cvf file is being ignored.