Did you download a patch or the full package? If you download a patch it would not give you any files relevant to this issue. The patch-option calculates differences between your version and the current version. The file in question in this case was checked into your existing version as part of the security fix, so it doesn't show as a difference.
I've looked at the code multiple times, and if you're downloading the full package, I don't see anything about the 3.0.11 > 3.0.12 upgrade script that would prevent you from reaching 3.0.12. Keep in mind there are 2 phases each to the 3.0.11 and 3.0.12 upgrade processes, and you should still be on phase 1 of 3.0.11.