A power loss during a register write operation is a plausible explanation to the phenomenon you're observing. This can cause corruption to the status and configuration registers, and could even lead to OTP bits being set in these registers.
The reason for this is that these registers are also stored in a NV memory area and this area needs to be erased and reprogrammed in some cases.
Therefore, it is highly recommended to avoid programming the device registers on every boot as detailed in the following Application Note: http://www.cypress.com/file/207641/download
Cypress Semiconductor Corp.
Customer Application Engineering