A couple of potential issues:
Do you have enough light to really see the front sight? I started shooting bullseye indoors, and didn't relly understand what the old-timers were talking about until I shot a few outdoor matches. The amount of light you have is critical to being able to focus on the front sight, at least in the beginning. Take a pencil and mark a line about 1mm below the top of the front sight. If you can't see it when you are shooting, you aren't looking at the front sight. If you can't see it at all, you probably need more light.
You may have weak eye dominance. You can help out by putting some semitransparent tape over your non-dominant eye, or shooting with a clear lens on your dominant eye, and a heavily tinted lens on the the non-dominant eye. The goal is to force your brain to depend on the strong eye, without totally occluding the non-dominant eye. As you get better and better at using the dominant eye exclusively, you can decrease the amount of tape or tint on your safety glasses. It's also possible that your eye dominance is so screwed up that you will always have to close one eye. There are something like 40 factors that affect eye-dominance, some of them as obsure as blood sugar levels and if you have to pee or not. Some people's dominance changes depending on what hand they are using. The brain is a complicated thing.
The sights should be aligned when the gun comes up. By trying to sit the front sight in the rear sight, your brain wants to look at the rear sight. As soon as you think "rear sight", you are going to be looking at it. As soon as you think "target", you are going to focus on the target. Think "Front Sight" and nothing else. If the sights aren't aligned as you come up to the target, you need to carve on your grips, so they are. A mind game that was very helpful to me was imagining that the front sight was attached to the trigger. As I pull the trigger to the rear, I imagine that the front sight also moves to the rear. The goal is to pull the front sight through the middle of the rear sight. Try it out. It's pretty a pretty weird thing when you start to actually believe that the front sight is moving.
Good Luck