My just turned 9 year old son has eye issues too. I was told by the psychologist and the optometrist who specializes in vision therapy that his scores were way low (overall 121 IQ) even though he tested verbally gifted due to processing speed. He has such a slow processing speed due to his eye problems, that it brought down his overall IQ. Even with these problems he just tested at 11th grade reading level, 13th grade reading speed, with a 90% comprehension (on vision testing)!. I too am wondering where exactly he would test if he could actually use both eyes at the same time. He turns one off and then the other very rapidly while reading etc., to avoid double vision, since his brain can't fuse the two images together. He has had surgery 2 times and had previously gone to vision therapy.
I definitely think you are going along the correct path when wondering if her eyes were the problem. I whole heartedly say YES!
You can read about my son under 'need help with scores' and 'trouble following directions'.