Even when you play the dvd on your PC drive? Any idea if you are getting good burns? What media and burner are you using? Make sure when converting you don't do anything else strenuous on your pc at the same time.
My own method using WinAVI is to batch convert, choosing "merge to one dvd". When it's done, I personaly want a menu. I delete all the .ifo and .bup files and put all the .vob sets (may only be one per episode depending on quality settings and size/length of original file) into their own folders for each episode. I rename each vob set so they are named the same as the first one that was created if you know what I mean. (VTS_01_1.VOB and if theres a second in the set VTS_01_2.VOB) I then open DVDLab pro and import all the .VOB's (choose the demux option), add them to movie boxes (make as many new movies as you need) and make a menu or menus for them. Menus can be as simple or advanced as you like.