This is a known problem due to the way GOP boundaries are calculated and whole encoding and how CC data is extracted. It can lead to progressively out of sync captions as each GOP boundary for each commercial cut puts the video ahead by a few seconds cumulatively.
For this propose I introduced two types of CC offsets. One which is a static offset which adjusts the initial offset (positive or negative)
Second is a Subtile segment offset which can be found under Settings -> Expert settings. This is a cumulative number which offsets the subtitle after each commercial cut. Try setting this to 0 or some other number till you find your sweet spot. This
helps to compensate for progressive shifting to subtitle after each commercial cut.