SPI flash chip failing without a 1M resistor from power pin to ground
Some things to think about and investigate:


Are you 100% sure that the SPI Flash chip VCC has a good solid connection to the power supply? 
Do you have the possibility that the part is actually being phantom powered up through the input protection diodes of the input control signals?
Check to make sure that the SPI Flash chip has a good solid GND connection in common with the microcontroller and the power supply.
Carefully check your design to see if you possibly have a potential silicon charge injection / latch-up condition caused by biased input pins to the FLASH part when the VCC of the chip is not yet applied.
Check during active communications between the MCU and the SPI Flash Chip if there are significant negative overshoots on the signal edges that go more than about 0.5V below the GND level as measured at the chip. Significant negative spikes can also disrupt the chip operation.