Could be DSDT issue (stuff happening in _WAK)... could be kext issue (all kexts can register for notifications of sleep/wake)...
BTW: The reason I go off time display for detection of lockup is that it will likely update even in the case the input system is dead. But hovering over the dock and expecting magnification requires the input system to work (mouse movement). And the mouse pointer moving on the screen is not indicative of a healthy input system (most operating systems handle this at a lower level such that it doesn't lag too much).
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