Really odd, but I can't think of anything that Qube would be doing that would cause this. This is using the 'Maya' jobtype, not the 'cmdrange' jobtype, correct?
I'm asking because if it's the Maya jobtype, Maya opens the scene, gets a frame number from the supervisor, sets the time slider that frame via the MEL currentTime, and then executes the render command. When it's done the frame it asks for another frame number from the supervisor, runs currentTime again, and starts to render. Once the job has started, very little changes.
Also, can you re-post the stdout, it was 0KB when you posted it before, and please also post the stderr output. perhaps zip them both up together and post the zip.
Have you tried opening a case with Pixar (or whoever provides support for RfM)?