Thanks! I've been playing KSP since 2012, but just got back into it after a long break.
I suspected it because it started after installing this mod, and then it never happened after removing it. After a few days I missed this mod so much I reinstalled it and then it happened again. I'm 99% certain no other mods were changed during that time, but I'm missing it again so I will probably try again and gather more data. All installed mods including this one are installed through CKAN.
It looked like the kerbal would start vibrating and then clip into the capsule it had just exited from before being flung away from the ship at high velocity.