OSX Store entitlement signing

I've been trying to update the app which is currently in the appstore but no matter what I try I get this issue:

code object is not signed at all

In subcomponent: myapp.app/Contents/entitlements.plist

The problem is that I have been signing the entitlements using this and it all goes through just fine:

codesign -f -v -s "3rd Party Mac Developer Application: My Company (XXXXXXXXXX)" myapp.app/Contents/entitlements.plist

codesign -f -v -s "3rd Party Mac Developer Application: My Company (XXXXXXXXXX)" myapp.app

codesign -f -v -s "3rd Party Mac Developer Application: My Company (XXXXXXXXXX)" --entitlements myapp.app/Contents/entitlements.plist myapp.app

I wrote myself step by step instructions last year when the original app was successfully accepted into the store but now it's failing so perhaps something within the process has changed.

I tried doing this:

spctl --assess --type execute myapp.app

which returned:

myapp.app: rejected

but I don't know where to go from here.

Any help is appreciated.