Search the forum for the caption sync issues (and this has been documented under known issues with workaround also), when you cut commercials the video goes out of sync due to GOP frame alignment (encoder issue). To work around there are 2 settings
you can play with.
1. Under Conversion Task -> Expert Settings there is an option for Closed Caption offset. This is a one time adjustment, as in if the caption are off by say 2 seconds CONSISTENTLY then you can use this offset to correct it.
2. If your closed captions are going out of syn progressively (2 sec after the 1st commercial, 4 seconds after the 2nd, 6 after the 3rd etc) then under Settings -> Expert Settings there is an option for Subtitle Segment Offset. This is used to compensate
for cumulative subtitle sync issues after each commercial segment is cut. So if after each commercial segment there is a 2 second additional correction required, then this value should be set to 2. Remember this is a cumulative correction, not one time. It
applies after EACH commercial segment is cut.
Once you've got this fixed you can use the Write chapters and subtitle option under Covnersion Task -> Expert Settings.
Remember all of the above only work with the latest 2.3.15 (older version have bugs in them). or later