I've come to the exact same conclusion as Bluenowhere. I'm playing on a pretty crappy computer, so I'm always on "Video Settings: Tiny," unless I'm surveying or exploring. The two times where I've experienced this lag-like, double-clicking phenomenon the most were 1) when I've been digging in and around heavily developed structures, and 2) when I discovered this elaborate system of water and lava tunnels about 50 layers down and tried to build a cobblestone road through it all. (The frustration of that attempt is what drove me to this forum, actually.) When I step out of the pit of death and away from all that "activity" and start laying blocks, the probably instantly disappears.
As several others have noted or implied, this does to seem to be a serious issue, because it's right when your structure starts getting developed that things start looking pretty cool. Pfft.