This is similar to another question that wasn't really answered: http://stackoverflow.com/questions/2738363/xcode-3-2-build-analyze-never-finds-any-issues
I used XCode's Build and Analyze for the first time on a large project and came up with a number of analyzer warnings. I corrected a few and wanted to verify my changes were being 'accepted' by the analyzer. I didn't even look at warnings in a number of files. But when I re-run Build and Analyze, all the warnings are gone.
I have tried: changing my compiler to LVVC GCC 4.2, switching from a debug to a release build, cleaning all (repeatedly), and quitting and reopening XCode. I just can't get the old warnings back.