Is it possible that you're uploading the code, running onInit, and then saving? That would cause Espruino to save its current state, which would then be out of sync with the modem that'd just powered on.
Try uploading your code without any call to onInit and see if that helps. Or use save on send: http://www.espruino.com/Saving
save on send
Can you also try adding the code Bluetooth.setConsole(1) to the onInit function and see if that helps at all?
Also, looks like you may be using at.debug() or some other debug option - it might be worth turning that off when you save as well?
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