After a successful schema comparison and deployment, I'm seeing a number of objects remain categorized as "objects that exist in both but are different". Looking in the differences pane for each item, the items appear identical. Why might this be happening? It doesn't appear critical, though it does somewhat diminish confidence in the product to see items that should be identical still marked as somehow different.
If it helps, my comparisons are between SQL Source Control (Subversion) and SQL Azure instances, and I'm seeing the same behavior for both staging and production targets.
SQL Compare version is 10.2.0.696.