Application Loader unable to unzip .ipa file

Question

I am developing under Flash Professional CS5, working on a PC.  Using the development distribution files, my application builds and I can run it on iPhone, iPad, and iPod.  Now I am trying to get it to the App Store.  I have a distribution certificate which I got before Apple pulled the plug, and was able then to just change the extension to .zip and upload to the App Store (where of course it got stuck until now). This week I rejected my binary in the store, and built an updated version.  You can't just upload to the App Store any more; you need to use the Apple Application Loader. This, of course, only runs on a Mac.  So, I downloaded and installed the latest version on my Mac. transferred the .ipa to a memory stick, and gave it to the Loader.
I get this curt message    "Unable to unzip application"
I have tried renaming it to .zip.
I have tried extracting the Payload and zipping that up again (different error but still no good)
Has anyone else got any applications built on a PC uploaded recently?  Please tell what you did

Answer 1

I had almost the same problem. I'm on OS X though. I have my issue solved but it took a lot of trial and error. There were enough clues on this thread though to get me there so thanks everyone. Here's what I went through and what I've discovered:
I compile with Flash CS5
(I was trying Christian's way on the commandline but I forget why I couldn't get it to work, must try it again now. ref:
http://blogs.adobe.com/cantrell/archives/2010/09/packager-for-iphone-refresher.html)
This creates my .ipa file. I don't know if I need to use the commandline, but I did in order to rename the .ipa file to a .zip file. I then double clicked the .zip in the Finder which unzips it with the default OS X app, not 7 zip or something third party. This produces a folder called Payload. If my swf is set in Flash to publish to Main.swf, then inside Payload I see Main.app
I zip Main.app by right clicking it in the Finder and select the Compress option, again, default OS X compression stuff.
This is the correct way to create the ipa file, and produce the kind of zip file that Application Loader wants.
Along the way, I encountered some other distracting problems. I'll explain those now, but they are not related to the actual ipa/zip/unzip problem.
I had two errors, one about a bad bundle ID. This was in fact a typo I had by one letter. In my case it was ca.abcd.abcs in iTunes Connect, and in Flash CS5's settings, it was ca.abcd.abc. That was a forehead slapper I tell you.
The other error was my app not being signed with a proper certificate. I knew I was using my app store certificate, not my dev certificate (this is important btw). I tried revoking my certificate in the app store as @JimmyInteractive mentioned, but I don't think in my case this was necessary. I still had the same issue after revoking. Avoid this if you can because it's a pain in the a$$ to set up all your provisioning profiles again on iTunes Connect and in Keychain, XCode etc. Prior to trying to get everything up onto the app store, I had of course been developing on my personal device, with my developer certificate. What I forgot to do for app store distribution, is in Flash CS5 change Certificate to my app store .p12 file. I still had it set to my dev .p12 file. Doh!
After I did that and figured out the zipping stuff it all worked. Hope this helps!