Unless there is a "clock adjustment factor" that Uprev accidentally over-wrote, I can't see where the tune would have any effect on the clock.
My guess is that the clock is a stand-alone unit and is just off by a little bit. Would probably cost more to grab time from ECM, over the CAN bus, than to just keep track of it internally. There may be an adjustment on the clock.
The FSM may have info on where the time base is and whether or not it can be adjusted.
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