Q:
Do the user alignment register values automatically store into flash or does it require a manual flash update?
A:
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After running the User Alignment function (GLOB_CMD[0] = 1), you need to issue a manual flash update command (GLOB_CMD[3] = 1) to store the alignment values into flash memory. The attached file provides a simple tutorial for testing this yourself. I hope that this helps. Good luck!
Best,
NevadaMark