On Chisels & Bits v. 8.7:

So, I'll describe my steps carefully:
Before:

After F3 + S (also happens with F3 + T):

After Server Re-Log / World Re-Load:

Notice how even after re-log, the metadata of the blocks is wrong: the stone bordering the glass is the wrong metadata, and the wool pixel art which you can see inside my house is pink instead of white.

Well that is odd I could have sworn I fixed this before...

Should be fixed in new builds.