xboard (HGM or others)

[hgm]

Yes, I guess it is just GUI overhead. One could stop both clocks during the GUI processing, as Matthew suggests. That would be fine in Two Machines mode. But it would not help when you connect to an ICS, and the ICS operates the clocks: when XBoard receives the opponent move from ICS when it is still processing the previous move it can delay starting the engine clock until it is done process, but that clock is bogus, and the ICS' clock is already running.

Note that -noGUI indeed does not affect the display in the Engine Output window, just the drawing and PV display in the board window, and the task-bar icon reversals. To suppress the overhead from the Engine Output, the window should never be opened. Once the window is created, it will be updated even when hidden, in case you would open it.