The weird thing with Hammer 4.x is that it made some adjustments to the way entinties and solids are created. If you placed a brush at a point (x,y,z) of the map, then Hammer will most likely try to mimic the SIZE and POSITION of the next brush as exactly as possible. So let's say you created a prop_phys with a model of a wooden crate (40.3u x 40.2u). Then the next time you create a brush, let's say in top-view (x and y), Hammer will try to:
a. Align the new brush in z-dimension to the same heigh as the crate you just created-
b. Make the brush 40.3 units HIGH.
That's just like it. Create a few brushes with sides divisible with 64, and you're fine, as Hammer will buffer those new dimensions instead of the odd ones you currently have.