I'm a 3D nerd, for what it's worth, so I may have some insight into one possible reason for blurriness. I also had problems with the 3D on FOP the first time I rode, and it took me some time to realize that glasses were partially to blame.
The glasses they use for FOP and several other newer 3D ride films are the Dolby 3D system, licensed from Infinitec. Their technology uses extremely expensive multi-layer filters on the glasses, and for some reason they really only work well when you look straight through the center of the lens, or a little to one side or another. If you move your eyes to look around the screen, as you look through the edges of the glasses you lose the 3D effect, and you get a "double vision" effect where both eyes see both the left and right images instead of the left eye seeing the left image and the right eye seeing the right eye image. This often registers as "blurry" rather than "double image."
This is only a small problem for people who don't wear glasses, because the Dolby 3D lenses are closer to the eye, and you're only likely to look through the edge if you have your eyes way over to one side or the other. When you wear the Dolby 3D glasses over your own glasses, the Dolby 3D filters are further away from your eyes, and it only takes a small deviation for you to end up looking through the edges of the glasses.
The solution is to move your head to look around rather than your eyes, and keep your eyes pointed straight through the center of the glasses. This is easier said than done, but every time you see a blurry image, that should remind you to turn your head, at which point the 3D should come back and the blurriness should go away, or at least get better.
My suspicion is that they only coat a small rectangle in the center of the glasses with the expensive coating, really to save money. Alternatively, it might be that the filters are sensitive to the angle the light is passing through, and when you look through the edges of the filter you're looking through the lenses at too high an angle.
I have verified this effect on Star Tours and on FOP; you can try it yourself. Deliberately rotate your head back and forth while looking hard at something with good 3D separation from the background. As your view shifts from looking through the center of the glasses to the edges, you'll see the 3D effect collapse and will see a superimposed double image instead. Rotating back so you're looking through the center will bring back the 3D. The section of Star Tours where the message from the rebellion is beamed into the cabin is a great time to look at this effect, as the messenger (Yoda or other) is strongly separated from the background and the switch from 3D to double image will be easy to see.
