Well, my answer was deleted because it was not the answer to the question. I don’t have enough points to comment on your question (what I tried to do because I obviously have no answer - the same problem as you, and trying to find out why we get this Invalid Binary error)
As I said in my first post: I will keep you posted. Today I created a new Xcode project with the same bundleID as the application that I have been trying to download for a week. It undergoes a preliminary validation on the server side, and I received a letter saying that "Waiting for a review." It answers one question that I had from the very beginning: this is not a server problem (I thought Apple had some problems with the pre-check process). I tried to play with architecture in this new project (for example, I use the arv7 arch for my application due to some incompatibility with the libraries of the third part). Still checking server.
Then I tried to copy the Info.plist file from my application into a new sample project that passes the server check: BANG -> Invalid Binary !! This info.plist is quite old, used with Xcode 3.0. I tried to remove some optional keys from it: the binary code is still invalid. Then I compared the original and necessary keys with the new project info.plist file: bang! The value "CFBundleInfoDictionaryVersion" was empty. In the new project, the value is "6.0". I just set "6.0" for the CFBundleInfoDictionaryVersion key and the boom, it worked. I assume Apple servers are checking the info.plist file and need the correct CFBundleInfoDictionaryVersion to read the .plist file. And I think that this does not happen with Xcode 5.1.1, they should have updated their server among the releases of Xcode 5.1.1, that’s all.
God, I can't believe how stupid it was. It is a pity that Apple does not provide comprehensive feedback. Hope this works for you! Let me know!