Well, when i started mapping i had the exact same problem as you can see here:
http://www.splashdamage.com/forums/viewtopic.php?t=14294&postdays=0&postorder=asc&start=0
although no suggestions actually worked, now i know what the problem was.
my brushes were not ‘snapping’ to the grid, instead it was all done freely which left a lot of overlapping brushes i guess.
As your probably aware you can change radiants grid size with the number pad. For something smaller you use the smaller grid, and larger grid for a larger brush, it just speed things up.
Just make sure when you create a brush, that it aligns with the grids grey lines exactly (i think its called snap to grid - i haven’t mapped in months so my terms may be wrong)
