Currently Being ModeratedDec 10, 2012 10:39 PM (in response to Ralpha.Zhao)
So, as a follow up to this - days of annoyance later. Here's how I got it fixed; hopefully this will be of use to someone else who encounters this. Unity3D was adding a couple of hidden files to the directory when building - I suspect this is because we're building the Mac binaries under Windows, but regardless of the cause; it has placed a couple of files named, e.g. '._unity default resources' inside the .app. Now; –
It appears codesign ignores those when verifying, but not when signing. packagebuild ignores them when building. So; the app verifies fine, and the package builds fine -- but if you install the package, then try verify where you just installed to, you'll get the "a sealed resource is missing or invalid" which iTunesConnect rejects the binary with. Add a --verbose and it'll point you to what files are misbehaving.
Now to go light people on fire...