To reproduce install ActiveState Tcl 8.5.9 and then build python using:
../configure --enable-framework --enable-universalsdk=/ --with-universal-archs=intel MACOSX_DEPLOYMENT_TARGET=10.6
Both 3.2 and 3.3 fail can be used. Install the framework and then open an existing file, use SHIFT+CMD+S to save the file and you'll see two dialogs (both labelled 'Save').
Some investigation learns that the save_as method in IOBindings gets called twice.
The attached patch (for 3.2) is a crude hack, but does result in a working copy of IDLE that doesn't show two save dialogs.
I'm inclined to commit the patch, it is a hack but there are already other workarounds for Tk-on-OSX weirdness.
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