Is your computer old, and/or is it under spec?
PC quite old. This is my third play through and now on level 20 and I have only recently noticed this problem.
It certainly did not exist prior to this.
If it's old, and the problem is caused by hardware timers, which it may or may not be, being a third play through is irrelevant. You could try toggling on/off your high precision timers (look up HPET), but that won't guarantee the problem will go away. Only an upgrade will do that.