Возможно дело в частоте конфигурационного интерфейса. Она, ЕМНИП, задаётся при формировании bit-файла.
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Determining the Maximum Configuration Clock Frequency
In Master BPI mode, the FPGA delivers the configuration clock. The FPGA’s master
configuration clock frequency is set through the BitGen -g ConfigRate option. The
BitGen -g ConfigRate option sets the nominal configuration clock frequency.
The default BitGen ConfigRate setting of 2 is recommended. This default value sets the
nominal master CCLK frequency to 2 MHz, which satisfies timing requirements for the
leading BPI flash families. The BitGen ConfigRate setting can be increased for a faster
configuration time, if the timing requirements discussed in this section are satisfied. When
determining a valid ConfigRate setting, these timing parameters must be considered: