This 'bootfix' program updates the Cubietruck boot code so it runs a Linux system stored in NAND. It changes the boot0 and boot1 code so it correctly detects the MBR and partitions created by the Sunxi nand-part software.
The program and required data files are included in the gzip file (link below) and all files are also available at Phelum on GitHub where the latest version is kept.
To run the program, extract all files to a directory and change path to that directory. If your PC is not a Cubietruck or compatible ARM-V7 architecture you will have to remove 'bootfix' (incompatible executable) and run make to create a version that will run on your PC. Once you have the program, connect the target Cubietruck to the PC (USB port on PC to OTG USB port on the CT) and boot the CT into FEL mode by holding the FEL button and then pressing the RESET button. Then run 'bootfix' and it will load the correct code into the CT. This process will take less than one minute. Afer the download the CT will reboot automatically. If the NAND has already been loaded the CT will start the Linux operating system. If the NAND is unloaded the CT will revert to FEL mode and you will have to boot it from SD card and setup the NAND MBR and partitions with your desired release.
This program avoids the requirement of using PhoenixSuit to load an unwanted operating system just to setup the CT so it can boot Linux from NAND. This program does NOT change any MBR and partitions in NAND and will not affect any Linux system (Sunxi MBR). But it will disable any Android system because the CT will no longer recognise the partition layout.
The master for this program is now at Github. The version there might be newer than what's here.