I have actually tried several programs to split MKV files. MKVMerge is the easiest and actually works, but I've recently run into a problem with it. I'm trying to split an MKV of one of the DVDs I'm backing up (made up of 4 episodes) so I set Merge to split after 00:23:42. Instead, Merge splits after 23:46, then 23:42 and so on at random times. I read that it has something to do with frame types, but I've never had this problem before. Any help would be appreciated.
I don't think it's random, I expect it's cutting on the closest key frame. If the key frames were every 300 frames and the time you elected was not on the key frame, then at 25 fps it could be a few seconds out. To cut between key frames would require re-encoding the video (optimally only around the cut point.) If every frame was a key frame the file would be much larger. I suggest you post at VideoHelp - there are more advanced users there. http://forum.videohelp.com/
Don't encode episodic DVDs as a single file. If the DVD wasn't ripped correctly, you can open the ripped files using DVD Shrink and use it's re-author function to re-author the DVD. In re-author mode you drag the title for each episode from the right pane to the left one. When you resave the DVD (using DVD Shrink's backup function) each episode will have it's own set of vob files so you can encode them individually. Just make sure before backing up the DVD again you go into DVD Shrink's options and change the target output size to DVD-9 or something larger. It's set to DVD-5 by default. Unless the target output size is larger than the ripped files you're re-authoring, DVD Shrink will re-encode (shrink) the video. You don't want it to do that. You want it to just copy the audio and video instead.
I wasn't trying to rip as a single file, it was simply the way the disc was formatted. It doesn't matter anyways, since I'm now using DVDShrink to rip and reauthor.