Partitioning is part of BSP building, probably the optimizatzion step that doesn't happen when you just rebuild geometry.
Make sure all your brush vertices are in the grid and that all brush faces are planar. Both things can easily happen when using vertex edit mode. Also, cone, cylinder and sphere builder, as well as the revolved shape builder from the 2D shape editor, don't give a damn about the grid, no matter how you configure them. Also, brushes intersecting at weird angles can sometimes anger The Goblin.