On Gazzetta's site appeared the timetable of each stage. There seems to be a few changes in the route. A spanish forum has them listed.
http://apmforo.mforos.com/1304540/10575373-giro-2012-ii/?pag=13
For those of you who can't read spanish, I'll make a brief recap...
Stage 1,2,3: no changes
4: the TTT has 1 km more, now it's 33.2 kms
5: the stage has 10 kms more, and the bump in the end (35 kms from the line) is changed
6: This is the most changed; the steep sterrato climb has disappeared

now there's only the shallow one, and it's somewhat further from the end. In addiction, there's a new climb between Montelupone (which is now further, too) and the finish. It is basically a hilly stage, perhaps better than the original but the sterrato is faded away.
7: 3 kms more
8: only change involves the category of a climb, but the route is the very same
9: 5 kms less
10: 1 km less and the climb at the beginning is not categorized anymore.
11: 12 kms more, the largest stage.
12: only a minor change involving the first climb of the day. 1 km more
13: no changes
14: 1 km more
15: 4 kms less
16: 1 km less
17: 1 km less
18: 10 kms more
19: 1 kms more
20: 1 km more
21: 1.4 kms less. Now it's 30.1 kms
Hence, stage 12, which was in doubt, stays almost as it is, while stage 6 changes drastically
