There shouldn't be anything in DisplayFusion that would be causing issues like that. In the log I can see the "WM_DEVICECHANGE" messages which are sent out by Windows whenever a device disconnect/connect happens on the system.
My guess is that one of the monitors is faulty, or has a faulty cable. When it drops out, it would trigger Windows to do a full display re-detection. If the monitor/cable is intermittently faulty, it could definitely cause Windows to do multiple re-detections in a row.
Try disconnecting one of the monitors, and leaving it disconnected for a couple of days to see if the issue goes away. If it doesn't, plug it back in, and try another monitor. Repeat until the issue goes away. Then you'll know it's either an issue with that monitor, or the cable for that monitor.
If that doesn't locate the monitor with the issue, it could be a problem with your video card, or even the power supply in the computer (maybe the power supply is starting to fail and can't give the video card enough power).
Hope that points you in the right direction, good luck tracking it down!