Ok, what I meant was... I know it's a container, but fansubbers coming out with only MKV files is very inconvenient for some of us. While they may think it's faster and easier, it's not helping some of us because of the problems you just mentioned. AVI's ALWAYS work and they should stick with them IMO.
I have yet to successfully merge AVI and .sub files but I'll give it a try sometime again.