Nothing unusual, it is just that the air cannot escape past the water in the tube and therefore the water cannot move down the tube. It will have filled halfway as the water would have been able to compress the air enough to move.
1. Make sure there is water backed up in the funnel and turn your pump on and off a few times. Should shift the water a bit.
2. Squeeze, wiggle and tap the fill tube. If you can break the water tension in the fill tube the water can slide down it, allowing the air to escape at the same time.
3. Slip a straw like object down the fill tube and into the res, this will allow the air a path out and the water to flow in. A bit like strawpedoing an alcopop. I used some small diameter heat shrink. This might be a bit difficult due to the 90° fitting on top of the res. Try 1 and 2 first.
Edit: Incidentally, did you know that you can mount that pump on it's back (inlet facing up) without any issues? This would allow some nicer tube routing if you ever felt like re-arranging things.
Edit 2: Welcome to OCN!
Nice looking rig you have there. Post your system specs when you have a minute (user CP > Edit System). It really helps people when they are suggesting things to you in the future.Edited by GingerJohn - 5/18/11 at 10:52pm