You will see AS configuration failure when Cypress® flash configuration registers are not set correctly or when programming file are not generated correctly.
For AS configuration with Cypress® flash S25FSxxxS, the flash configuration registers (CR2NV/CR2V) should be set to the following before configuration start:
0x8A (ASx1 scheme, 4 byte addressing, dummy clock cycles 10)
or
0xC8 (ASx4 scheme, 4 byte addressing, dummy clock cycles 8)
The flash configuration registers can be configured by external processor or other hosts.
Meanwile, Programming Object File(.pof) or Raw Programming Data(.rpd) should be generated with 'disable EPCS/EPCQ ID check' option enabled.
For Cypress® flash configuration registers detail information, refer to Cypress® flash datasheet (e.g. S25FS512S).