If you guys can help me do some tests in chat some time when I happen to be around, I could possibly try to pinpoint the issue if it is indeed on my end. We'll do some experiments and see what specifically causes breaking if it's possible. If you guys ever manage to get free time please drop by.
ffsplit just uses ffmpeg, and ffmpeg doesn't really ever generate any erroneous output, and twitch is also based off of ffmpeg internally, so it makes sense that it would work. I don't use ffmpeg so I am doing things "on my own" so to speak, but I should be able to pinpoint the issues if you guys ever have time for testing.
I just have no other choice than to do some in-depth testing with you guys. Would be greatly appreciated (when I'm around, which is almost always). Sorry I didn't suggest doing this sooner, I had been waiting for twitch to get back, but they can't do anything until after the new year.
Let's see if we can get this problem fixed, gentlemen.