As far as I can tell this is a 100% lumen/shadows issue.
If you have light sources which produce shadows, you will probably get vastly different shadow rendering per eye; either shadows in one and not in the other, soft shadows in one and hard shadows in the other, or any flickering nausea inducing combination of these things.
Disable ‘casts shadows’ for the lights, and the problem goes away (along with all your shadows of course!)