The symptoms are strange. However since the pins are not exposed, probing with logic analyzer is not possible. Will need to run test codes specifically. By the way have you tried other libraries? I suppose there should be other libraries for generic serial/SPI flash on Github. We may also treat it as a simple SPI device and run SPI commands to test it.
Flash pin 1 => CS
Flash pin 2 => MISO
Flash pin 5 => MOSI
Flash pin 6 => SCLK
However I am unsure if the SPI port can be remapped.