The mkv was encoded using a variable frame rate, so AVStoDVD cannot give a fixed frame rate for it.
When you look in the previous dvds you've made in AVStoDVD it should show the complete set of .ifo, .bup and vob files. This one has not been authored properly.
To fix this we need to merge the vobs into one file and try to author it again in AVStoDVD. You've already done the hard part of encoding the video to fit dvd specs. We just need to take the various parts and reauthor.
The problem is that we need to use programs that look for the .ifo files in dvd structure. The file that is named VTS_0_01 and looks like an mpeg file in your computer is actually the .ifo file that we need to use.
You can try a program called PGCDemux. Use this VTS_0_01 file as input in the program and make sure to set the program to demux the audio and video streams and the subtitles. You might have to rename the file with an .ifo extension to have it recognized. If it will process this, you should have separate streams for each of those. Do you still have 4 different subtitle streams in this dvd?
If this will demux everything, you can import the streams back into AVStoDVD to try and build the dvd structure again.
I don't know that this will work properly.
Another way to try this is to merge the vobs with VobMerge. Then use this combined vob file as input to AVStoDVD and try to reauthor. The problem is you might have to import the subtitles separately. And to do that you might have to extract them from the original mkv file using Mkvtoolnix and MkVExtractGUI2.