MAS codesign requirements break Java app signing

[Zach Oakes]

It looks like Apple has changed its codesigning requirements for the Mac
App Store. Thus far, I've been packaging my Java app using Oracle's
appbundler tool and signing it with the following script:

http://pastebin.com/BtLV9bur

This worked fine even as recently as last month. This time, I get an email
from them with the following:

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 think this error is incorrect, because I'm using 10.9.5 with the latest
Xcode (6.1). I tried "codesign -dv MyApp.app" and it says "Sealed Resources
version=2 rules=12 files=7", so I think I am using v2 signatures. My JDK
version has not changed since last month (8u25), so I can rule that out.

I would appreciate any help. Thank you.

Zach