I've been testing 4.0.4 for the past 2 weeks with transcoder on live streams from FMS. I've noticed that from time to time, the different bitrates in the abr (160p and 360p) sometimes develop slight discrepancies in segment durations.
For example, here's a diff of the output m3u8 |grep EXTINF for 2 transcodings of the same stream running for 20 hrs:
[stg-cache-01 wowza]$ diff /tmp/live_160p.m3u8.extinf /tmp/live_360p.m3u8.extinf
The target duration in this case was reported as 6 but the segments appear to be a bit under 4. So this means the difference occurred after approx 5.7 hrs.
I've been running 24 hr tests. I've never seen a difference totally more than 90ms overall in ~10 x 24 hr runs.... but similarly, the majority of the time, I don't see a 0ms difference, which would be what I would expect -- with all key frames starting each segment aligned exactly. 40-80 ms is typical and it's always been only 1 segment that differs. Sometimes it's even the first segment (which seems to suggest it isn't always long running streams).