I too am a beginner and I had this exact problem - eventually I figured out that my initial actor (the box BSP) which I used to make my floor, was not properly aligned with the grid. If you start with one actor that is not perfectly aligned, then of course the grid snap will tend to be a little off for any other actors which are meant to seem up with that or first actor or any other related actors.
Seems like there could be some shortcut for the alignment of the first actor, but this seems to work well for me now!