A fault tolerant storage controller having a processor, redundant copies of a stored program, and a timer that automatically runs when the processor is reset is disclosed. Selection logic selects a first copy of the program to boot on the processor. If the timer expires before the first copy successfully boots, the timer resets the processor and re-enables itself to run again. This time, selection logic selects a second copy of the stored program. In one embodiment, the program comprises separate loader and application programs, each having a redundant copy. The loader re-enables the timer when jumping to the first copy of the application code. If the timer expires before the first application copy successfully boots, the timer resets the processor and re-enables itself to run again. This time, the loader selects a second copy of the application program. In one embodiment, the redundant copies are stored in separate FLASH devices; in another, in distinct regions of the same FLASH device.