You can try adding this to your profile
CommercialMergeTool=avidemux
The default is ffmpeg which works great for most video files but for files which have large GOP intervals it can cause the kind of issues you’re seeing where commercials are cut mid GOP. The difference is that while it may fix your stuttering the cut location will not be exactly at the point you marked. This is because it’ll wait for the next GOP frame to get a complete picture, which may be a few seconds after the identified cut point depending on how far apart the GOP frames are in your recording.