Hi.
The bottom while loop does indeed run at 1 Hz. This is enforced mainly by the Wait for PPS node.
The top while loop should continue running at 51.2 kHz. In that loop all you'll have is a sequence structure with the analog sampling in the first frame and Get Time.vi in the second frame.
By the way, another thing to check: what is your top-level clock frequency? The timeout values in the bottom loop assume your top-level frequency is 40 MHz.If it is a different frequency, then the timeout values must be adjusted (ie. if your top-level frequency is 80 MHz, then the timeout for the Wait for PPS node should be 82M and so on).
Regards,
Alejandro