I found the problem: https://github.com/LowPowerLab/SPIFlash/issues/16

The sketch I used to verify the SPI Flash was missing a SPI.begin() in setup().

I hooked up a logic analyzer and discovered that there was no activity on SCK, MOSI and MISO when trying to use the SPI Flash.

Wrote my own sketch that only reads the jedec id from the SPI Flash and it worked. Must be something with the SPIFlash lib version.

Attaching a screenshot from the logic analyzer showing the jedec id read from the SPI Flash.