Are there any known issues with the Parallel Flash Loader (PFL) in the Quartus II software version 12.1SP1 when data is read from an EPCQ or Micron QSPI flash device?

Yes, there is a known issue with the PFL in the Quartus® II software version 12.1SP1.  When data is read from the EPCQ or Micron’s Quad SPI flash device, signal contention between the PFL and the flash device is seen for several pfl_clk clocks at the beginning and end of data being read from the flash device.

A patch is available to fix this problem in the Quartus II software version 12.1SP1. Download and install patch 1.64 from the appropriate link below:

• Download the version 12.1 SP1 patch 1.64 for Windows (.exe)
• Download the version 12.1 SP1 patch 1.64 for Linux (.tar)
• Download the Readme for the Quartus II software version 12.1 SP1 patch 1.64 (.txt)

You also need additional timing considerations for flash_io and flash_ncs as shown in the timing diagram.

This is fixed in the Quartus II software version 13.0SP1.