Resulting video is bad always on the same place
Two possibilities that come to mind are that it could be a dropped frame that isn't that noticeable until an H.264 compression is applied or it could be that you are using an insufficient bit rate and that particular part of the video has enough going on that it couldn't compress well.  

I would check the time code around the problem to make sure all the frames are there.  I would also try increasing the bit rate used and try VBR 2 pass and see if either of those fix it.