Kariudo wrote:h.264 in avi is a bad idea, and unless you used some specific settings of x264 editing with it is a bad idea as well.
If you still have the original files, toss out the ones that AVS converter gave you. Then, use avisynth to load your original files into vdub and make lossless clips (using UTvideo, lags or huffy). Entire episodes can be converted if you have the time and space, but you're gonna be making clips anyway...so you might as well do it now.
I did load one of the AVI files into Virtual Dub and converted it to LAGS, but it won't load in WMM. I was making a WMM AMV before I formatted, but it I have to use Vegas then I will do that. The Lagarith file I converted with AVS work, but the one I made in Virtualdub won't for some reason.
I really have no idea how to use AVISynth and I have tried before. I'm also not sure what else to use for MKV files.