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Based on the error you are seeing, my guess would be that your command line build is using Xcode 4.2 or older tools while you are running Xcode 4.3 for the builds that work.

Xcode 4.3 bundles up the command line tools inside the app to make it a simpler install. But this makes command line builds harder. You can install the Xcode 4.3 command line tools either by the standalone dmg available on Apple's site or via the Xcode “Downloads” preference pane (in the “Components” segment).

Another possible fix might be to let the command line tools know which version of Xcode to use. In Terminal you should see something like the following:

% xcode-select -print-path
(which may differ based on where you installed Xcode 4.3).

If you don't see this, then you'll want to do:

sudo xcode-select -switch /Applications/
(which will automatically append the Contents/Developer components).

I hope this helps!
CTO, The Omni Group