It interesting that I am also having an identical issue. I have been using Mezzmo for around 10 years and in the past year or two I starting using Roku as the client interface. I am now seeing this repeat (30 to 60 seconds) during most movies around the 1 hour mark (52 to 78 minutes) and again around 15 to 30 minutes later. I have logged the transcoding and I have been seeing the "Child process ended with code: 109" listed in the log file about the same time the movie does this 'repeat'. This has been now going on for at least 3 to 6 months and I didn't know if the router or computer was going into some type of sleep mode even though they are set up not too. Now it looks like this issue may be tied to Mezzmo which may be helped by using a Roku client. Note this 'repeat' issue is see on multiple TVs using the same Roku version hardware (Roku 3), I have not tested it using other Roku hardware.
Hardware Specs:
Atmel Processor 8 -core
16GB Memory
4 x 5GB drives
Win 10
Mezzemo Ver. 5.2
Roku 3
Multiple clients running hardwired and WIFI