Intel Binary and Mac Store codesign

I have a stub project that consists of a few xtras and the following bit of movie script code:
on startMovie
_player.searchPathList = [the applicationPath & the applicationName & ":Contents:Resources:"]
_player.searchPathList.add(the applicationPath & the applicationName & ":Contents:Resources:Branding:")
_player.searchPathList.add(the applicationPath & the applicationName & ":Contents:Resources:Zoomups:")
_movie.go(1, "main")
end
This stub is how we've always done our Mac builds, just adding some files to the .app in the Contents/Resources folder, from a windows build, and it's all good. Then the Mac App Store came about and this recent Director update allowing us to build Intel-only binaries for the store. The problem arises during the codesign step for the Mac Store. If I build my stub as Universal Binary, the codesign process is fine, and we can submit the app fine, but of course it's rejected because of the universal binary. When I build the stub as Intel Binary, the codesign process fails with the error:
codesign_allocate: the __LINKEDIT segment does not cover the end of the file (can't be processed) in: (*path to the .app*) object file format unrecognized, invalid, or unsuitable ?
Has anyone figured a way around this? I'm stuck at this point.

Did you figure this out? I wonder if I can apply the same solution for an AIR project

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