It is as if the Animator is waiting 3 sec. to see if you are going to make further clicks, before triggering the final ($ControlActiveSetting == False) update. Indeed, one can see that there is a delay after hitting the plus button (or minus button), before ControlActiveSetting is changed from True to False; almost immediately after the setting changes, the plot is updated.
Manipulate[{Dynamic[$ControlActiveSetting],
Plot3D[Sin[x] Cos[y], {x, 1, 5 a}, {y, 1, 5 a}]}, {a, 1, 5}]
This can be confirmed with LinkSnooper as well. I could find no $FrontEnd options or SystemOptions that might control this delay.
My guess is that the delay allows the user to adjust several controls before a high-quality update is triggered. Since these might take a long time, I assume Wolfram thought that a three-second (or whatever) delay is an appropriate compromise.
Update: Addendum
I probably should have pointed out, especially since it is not often mentioned, that by default, plots depend on $ControlActiveSetting because the default option setting PerformanceGoal -> $PerformanceGoal has the value
OwnValues[$PerformanceGoal]
(*
{HoldPattern[$PerformanceGoal] :>
If[$ControlActiveSetting, "Speed", "Quality"]}
*)
Anyone using Manipulate with plots will be familiar with the effect. This and the system setting $ControlActiveSetting to True when a control is operated are the causes.
Sin[x] Cos[y]is an example actually in the documentation. – Michael E2 Feb 01 '15 at 14:17