Cannot upload IPA to store after updating Mac OS X to 10.9.5

I need to update an app on App Store, but the Application Loader keeps rejecting my IPA.

The command I'm using for the build is the same one I used before one of my colleagues updated the Mac OS X from 10.8 to 10.9.5.

"/Users/imac/dev/AIRSDK_Compiler/bin/adt" -package -target ipa-app-store -storetype pkcs12 -keystore  /Users/imac/Documents/flash/dist/distributionCertificate.p12 -storepass notShown -provisioning-profile /Users/imac/Documents/flash/dist/Monster_Brain_Dist.mobileprovision Monster_Brain_Surgery.ipa monster-brain-surgery-app-ios.xml Monster-Brain-Surgery-Mobile.swf Default.png Default@2x.png Default-568h@2x.png Default-Landscape.png Default-Landscape@2x.png assets -extdir /Users/imac/Documents/flash/monster\ build/lib

I checked all the certificates and provision profiles and they are good. I tried transforming the ipa into a zip, uncompress it, compress it to a new zip and transforming into a ipa.

I also run the command:

codesign -vv Monster_Brain_Surgery.app

and it says Monster_Brain_Surgery.app: resource envelope is obsolete

I can't seem to find any solution to this specific problem online. If anyone ran into this problem, I would appreciate any help to make it work.

EDIT: I'm using the latest AIR SDK.