If you are seeing any issue with booting FX3 from a SPI flash then please make sure that there are no pull up/pull down resistors on the lines MOSI and MISO. If you are using the FX3 DVK then check for resistors R246 and R252. If these resistors are populated on the board then try by removing them. Then FX3 should be able to boot from a SPI flash with out any problem.
Let me know if this does not solve your problem.
Please note that earlier versions of FX3 DVK have these resistors populated. If so, please remove them and then SPI boot should work.