I had some difficulty merging these as well.
You need to perform the merge action first, before applying any other processing – immediately after ripping.
I had to use a trick on one of those movies, before I was able to merge them: use MKVtoolnix to cut 2 seconds from the beginning and end of the files. I assume that the length of the video and audio streams was not perfectly the same, so that a few frames were missing inbetween the two parts
