I have an EOTech 512 and a Vortex VMX-3T (3x) flip to the side magnifier. For some reason, when I look through the magnifier with both eyes open, I see two targets; one magnified and one not. When I grab my walmart scope thats on my .22lr, I can look through that with both eyes open without a problem. Is there something I am doing wrong/something I can adjust to fix this?

I'm right handed, right eye dominant.

What's the magnification on the .22lr scope? In my experience lower magnification makes both eyes open shooting harder because the images from each eye overlap each other more closely making it harder to discriminate between the eye behind the optic and the one that is not. With higher magnification the images are so different that I can tell which image I need to focus on.  Hope that helps. YMMV

ETA: holy shit I didn't mean to necro a 4y/o thread. Why hadn't anybody answered this poor guys question?