I'm sorry to hear you are having trouble with this project! Can you clarify what kinds of speeds you are measuring? That would be helpful to know.
I can think of a few possible issues. Are your magnets all lined up so their north and south poles are pointed in the same direction? If not, make sure that they are.
In the Science Buddies version of this project, the magnet stages are 10 cm (4 inches) apart. This is farther apart than your magnet stages. I've done the project using the procedure described in the Science Buddies Project Idea:http://www.sciencebuddies.org/science-f ... ml#summary
When I built the Gauss rifle, the magnets I used were strong enough that if the magnet stages were closer than 10 cm, the attractive force between then would pull the magnets together. If you have your magnets 2.5" apart and there is no tape holding the magnets in place, then the magnets may be weaker than the ones I've used to do this project. If that is the case, then you might try N52 neodymium magnets.
You'll want to make sure that the two ball bearings at the "launch" end of the rifle are right up to the edge of the dowels, like in Figure 2 of the procedure I linked to above.
Let me know if you still have problems after you try these things - also, you could post a picture of your setup as an attachment to a post, and that might be helpful for seeing what is going on.