Well, first of all, thanks for uploading the series.
Second, I know how frustrating it can be to play MKV files. But, like many have said it is in fact a better quality file format and is worthwhile, if you like your anime in high quality.
Obviously though, the great size and troubleshooting it needs sometimes when things come up (for certain people) will tend to give problems.
If you have downloaded MKV files and really wish to keep it in AVI at all costs (maybe you want to watch using your DiVX player or something), then recently I've made a perfect conversion between MKV - AVi, while hardsubbing the subtitle file and keeping quality + subtitle + sub style and everything, perfect. Well, that, and a significantly lower file size.
How? Well, its gonna be tough writing the steps here so here you go, my blog:
Click here
Please try it out, I've even included pictures and download sites for the program. Sorry to somehow advertise like this but I really wanted to spread the word. This is, by far the best method I've found the convert MKVs to AVI.
Feedback are welcome.