Do you actually want them as avi or would you prefer a dvd that plays normally? If you convert each one separately in AutoGK, you could splice them together afterwards with Vdub. I’m not guaranteeing that you will get a seamless video out of all of that though.
I’m not sure why they are working as individual vobs and not as a whole. There is definitely something screwed up in the structure of your dvd. What I might try next would be to combine the vobs you got out of FixVts into one mpeg file and reauthor.
How you do that depends entirely on which tools you have. Vob2Mpeg is a free tool that can normally do this process, but your dvd isn’t what I would call normal. If you do get it to work, you can reauthor to dvd format. Do you have an authoring program that you normally use? If not, try the free trial of TMPGenc Author 3, or DVDLab Pro’s free trial, or one of the free programs like DVDStyler or GUIforDVDAuthor.
If Vob2Mpeg doesn’t work you might try importing the vobs straight into DVDLab Pro, and let it demux and combine the vobs.
Or use VideoRedo Plus. VideoRedo Plus can work with vobs if you check the box in Options -->Enhanced Plus Features to “auto combine sequential filenames”. The output from VideoRedo can be either mpeg2 or dvd format, whichever you would prefer. And if you use VideoRedo you could also try the Quickstream Fix tool on this mess of a dvd you have. There is a free trial for this program as well.