Is it possible you have another encoder on the same network pushing packets for the same channels, which could be causing a conflict? This behavior makes it look like some streams are losing packets.
Do you see multiple errors like this:
server WARN 200 - RTPDePacketizerWrapperPacketSorter.packetLoss\[live/_definst_/streamOne.sdp:trackID=2\]: last:13066 curr:25584
server WARN 200 - RTPDePacketizerWrapperPacketSorter.packetLoss\[live/_definst_/streamTwo.sdp:trackID=1\]: last:63732 curr:14634
Another troubleshooting tip: Note the big discrepancy between the last and current values. If RTP, the values should be similar. The packet sorter only works if the stream is RTP. We use a sequence number in the RTP header to do packet re-ordering. Because the numbers are so far apart, it most likely means that the stream in question isn’t RTP. Possibly the stream(s) that are causing these issues are MPEG-TS that aren’t RTP-wrapped.