In HW Config you can enter a correction factor in the "Clock" field via CPU > Properties > Diagnostics/Clock. This affects only the CPU's hardware clock. With the correction factor you can correct a time deviation (clock is "fast" or "slow") within 24 hours. You can enter positive or negative values in ms.
The influence of the ambient temperature on the quartz frequency causes the inaccuracy. Given the large temperature range (such as in the control cabinet) within which the S7 controller can be operated, this effect is more pronounced that on wristwatches, for example.
If the clock is 4 seconds slow after 24 hours, you need to enter a correction factor of "+4000 ms".
Cycle interrupts are derived from the system clock and have nothing to do with the hardware clock settings. More information is available in the HW Config Online Help (Help button in the relevant tab of the CPU's Properties dialog).