Every one of these trucks do this at some point in time. Mechanically you have zero issues. Does it make an annoying noise? Absolutely. But that's about it.
My unproven theory is that the actuator moves the VGT out of range post-tuning; causing the system to attempt to move the nozzle back into range.
The only way to prove that would be a running data log from stock until the problem occurs.
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