What exactly do you mean by "surges"? Large amounts of EMI can erase the flash chip/corrupt it, causing what you are seeing.
yes i know it. but why it is not happening with atmel controllers which are also non automotive grade.
Depending on the physical orientation, chemical structure of the chips, placement on the board, stray cosmic radiation, code running, EMI reception of the electronics circuits, shielding (if any) of the flash, oxidation levels, wear level, power levels, etc.
It could just be that you got lucky with the Atmel controllers not being affected by the test scenario; It could be they are being effected, but in a different way; It could be that there is something else causing corruption of the cypress chip. There are too many things that could cause it imo.