Questions about An65974

Hello:

    I tested AN65974,but failed. And i have two questions:

   1.There are some reasons that I must programed FPGA first.I programed FPGA.After that I programmed the FX3S device. When  FX3S device finished programing，I reset FPGA.Does the order affect the result?

   2.After programed,the flaga is high,flagb is low,flagc is low,flagd is high.Please tell me how does this happen？

​   Thank you very much.