I had this issue a few weeks back, only happened once and ever since I've not had an issue. I had the layer set as a preset and when I re-fired the preset everything was happy again. I had two identical systems going at the same time with the exact same content and TC input, it happened on the primary but the backup didn't have the glitch, thankfully I was in program mode not show mode at the time. I chalked it up to a random issue, but created a second preset trigger based on timecode one second after the first trigger just to help avoid this in the future.

If you ever get a better answer let me know, I'd love to actually know what was going on.

The current show I'm running is a single 1920p60 output with 4 layers, 1 mix.

Im running MP 5.1 2.8GZ with 8GB ram, 2 SSD (one content, one OS), Cat 466b.