Examined the circuit.
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Feb 25 2017
There was a behaviour change in the logic a few releases ago, that made it more reliable (in terms of preserving signals), but also gave it the ability to preserve too many signals in large circuits and lockup the logic processing.
That would exactly explain the working state for a "fixed loading time".
Feb 24 2017
Tried that behaviour a few times with large groups and watched them closely.
Could not reproduce the error,
unless I alt+f4 while the block operations are in progress,
and thus destroying my action-queue in mid of its processing.
Feb 23 2017
Can you reproduce this without using an exploit clock?
As any signal triggering more than usual updates (especially visual active updates) it will run into an anti-spam mode and if it does not recover from slower operation it will stop working completely.