What you are describing is a typical problem at the layer break. This is usually a problem with the type of media you are using, though the burning program can affect this as well. On dvd video the layer break has to be positioned correctly, at the beginning of a cell.
I recommend Verbatim brand DL media as the best choice. The only other type I might use would be Falcon DL, but it is not as widely available.
I also recommend burning with ImgBurn. It will position the layer break correctly.