I couldn't track down which sequence you are talking about, but I may have an answer:
On FPGA, everything in a timed loop executes once per clock pulse (40 MHz). If your sequence is inside a timed loop, everything will execute at 40 MHz.
If it is a regular while loop, it will not execute that fast. Code is relatively slow outside a timed loop. If I understand correctly, each operation or two takes a clock cycle. Your entire while loop rate could be many clock cycles depending on the complexity of the code.
Bruce
Bruce Ammons
Ammons Engineering