Apple says I'm signing an app with old OS version, and I'm not

I'm trying to submit a Java-based app to AppStore. After having the worst headaches in my life trying to sign everything my last problem (I hope!) is this:

Invalid code signature - Signatures created with OS X version 10.8.5 or earlier [v1 signatures] are obsoleted and will no longer be recognized by Gatekeeper beginning with OS X version 10.9.5. To ensure your apps will run on updated versions of OS X they must be signed on OS X version 10.9 or later [v2 signatures]. For more information, see OS X Code Signing In Depth

I don't understand this message because:

1) I'm running a 10.10.1 version

$ sw_vers -productVersion 
10.10.1

2) and my app is signed with version 2 signatures

$ codesign -dv MyApp.app
Executable=/Users/jess/git/http://ift.tt/1B2bOqw
Identifier=com.myapp
Format=bundle with Mach-O thin (x86_64)
CodeDirectory v=20200 size=286 flags=0x0(none) hashes=5+5 location=embedded
Signature size=4351
Signed Time=20/2/2015 16:31:42
Info.plist entries=20
TeamIdentifier=D38HW9S49C
Sealed Resources version=2 rules=12 files=15
Internal requirements count=1 size=204

(You can see the line saying Sealed Resources version=2 rules=12 files=15)

So, what is the problem ? What am I missing ?

Thank you