Polarisation might be part of it for you, though there probably isn't any polarisation in e-ink screens - I could be wrong, easy to test with some polarised film or glasses. There are some big threads on here on polarisation that are worth reading if you haven't already.
There are two other factors to consider, people sit far away from projectors which can help with eye defects, and the resolution of your projector is low which could help a bit too. I used to have a tv that was much more comfortable when watching non hd channels.