i beleive i waited two or three hours for the inital test, one hour after changing to my underground design, and one hour after changing the "sky" blocks to dirt.
Again your design may still work, as it is certinly more compact, we may want to try that out... you know what? i'm going to go murder all but two of that test village and change the burried portion back to your design. ill let you know how it turns out.
Edit: Nevermind looks like you already started that. The doors might be the wrong way though, so i'll flip those at least, i beleive i experianced problems when the doors were closer to the "inside" space then the "outside" one. or i might just be paranoid.