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As Gerhard suggests, look at the manual and the reset state of registers.
Remember also that some pins may be probed for specific interfaces by RomBoot, and BMS may alter NOR memory interfaces. AT91BootStrap might look at specific pin states, and setup extended SDRAM buses, etc.
If you have some critical hardware attached, make sure it can see a power-on-reset type signal, and perhaps guard the functionality by driving a specific pin, or latching a state, once the system is up and running, rather than in indeterminate state as the power supplies sequence up.
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