http://blog.twitch.tv/2014/08/3136/
TL;DR: Twitch now scans VOD's for copyright infringement in 30-minute blocks(0:00-0:30, 0:30-1:00 etc.), and if it finds any, it mutes the whole 30-minute block. Imports will also be muted. No mention of whether infringements mean bans or not, so you should prepare an alternative stream on a different site just in case.
TL;DR: Twitch now scans VOD's for copyright infringement in 30-minute blocks(0:00-0:30, 0:30-1:00 etc.), and if it finds any, it mutes the whole 30-minute block. Imports will also be muted. No mention of whether infringements mean bans or not, so you should prepare an alternative stream on a different site just in case.