Day 6 after the reboot and I think this is happening again:
Note the CPU usage of the parent mate-panel process.
Also note the SWAP usage: this system has an SSD with vm.swappiness=1 added to sysctl.conf.
I now think this might occur because of a weird interaction with the Eye Of Mate image viewer.
I have a massive slideshow running on one of my screens, and the CPU spikes are following the image transitions.
I will attempt to reproduce on my work machine on Monday and if I manage to do so, I will create steps to reproduce for a future bug report.
Edit: in the mean time I'm gathering some logs of top running in batch mode. I will let it run for a few hours, monitoring the eom and mate-panel memory usage and pause eom for a while to see if the memory increase correlates with the period of activity of eom.