The efficiency tools were nerfed in the most recent official update, 1.4.6, so that the only work on their respective block types.
However, when playing in SMP, the efficiency of tools is the same as it was before...to the client, yet the server has the nerfed tools. This means that the server doesn't actually register the block as "destroyed" until after it's supposed to be, or even not at all, and the client still believes the block is gone, causing the "invisible block" glitch that used to happen in some of the 1.4 snapshots.