How to trigger:

  The bug can be triggered by simply destroying some blocks. That will cause random flickering "ghost blocks" to appear, that can be passed through. Some of them are previously destroyed blocks, and some are ghost flowing water blocks, that can spawn either in the shape of a box, or a waterfall.

  It gets worse if the option "Use VBOs" is turned on, but the bug happens regardless of it. The ghost blocks dissapear after toggling that option.

Video settings used:

Graphics: Fancy
Smooth Lighting: Maximum
VSync: On
Render Distance: 4 chunks
Bobbing: On
Advanced OpenGL: Off
Clouds: Off
Mipmaps level: Off

Also, there are no mods installed.

  Below is a video showing the problem (it happens in survival worlds, too, and also while breaking blocks manually). The lag in the video is due to the recording program.

Sorry for my bad english.