You could try removing trakt just for testing purposes to see how that might impact this.
After thinking about this I decided to try something a little less invasive.
On my two backup servers I changed the update interval to only once per day at 03:00 as I can fix the little differences if needed.
Also I changed the interval to twice a day for my main server at 22:00 and 09:00.
I figure that somehow the updates were getting out of sync and part of the "play" info was getting scrambled.
Until you mentioned it I did not thikk of Trakt but the update interval was 15 minutes for all it is possible that was scrambling continue watching.
I will run like this for a while and see what happens.
I figure that in the event of a failure of my primary server the two backups will only be a little out of sync and I can easily fix that if needed.
I am sorry that I cannot test as you suggested but I am too paranoid about a computer failure ruining my day. I will test the drastic situation of completely removing Trakt if it turns out to be needed.
BTW: I only use the TV show side of Trakt but that is where the problem is so that bit of info is of limited use.
It is the old case of: "I'm paranoid, but am I paranoid enough."