Answer:
When the runtime system is at the point of unblocking or blocking a thread, and busy in changing the scheduling queues, then it would be the most inappropriate time for the clock interrupt handler to start checking those queues for thread switching, since at this stage threads may be in a highly inconsistent state.
One of the solutions can be to set a flag when runtime of the system is entered, so that the clock handler can see this and can set its own flag, then return to its original position. After the runtime system has finished its working, it will inspect the clock flag and will see that a clock interrupt has happened, and then run the clock handler.