Unaligned mesh.

M

Hello,

I'm having a bit of bother with my mesh. Basically, my model consists of a cylinder with a smaller box of same length subtracted from the inside but retained. In other words, I used the subtraction tool in gambit to create a box that fits perfectly inside the centre of a large cylinder, and is the same length. After I've made these two volumes, I want them to act as one fluid. The reason I am doing this is I need the mesh structured in a certain way, as this is part of a bigger model.

The problem is, they don't act as one fluid if I mesh them one at a time. They act as two independent volumes. The meshes don't line up even though they share the same face. Even if I do get the meshes to line up they still act as independent volumes. Any idea whats happening?