when I turned on VBO textures, random stuff would randomly flicker and the skybox would be visible through it. this did not happen on my laptop (intel core 2 duo with onboard graphics)
Environment
Windows 7, Intel core i7 3770, intel hd graphics 4000, Java 1.7.0_45 64-bit
Are you getting FPS drops too?
Also, Minecraft gets a similar display issue when I switch resource packs or the game crashes. The workaround has something to do with killing the right javaw.exe processes, but it's too random to perform reliably.