Codesign in Mavericks (10.9.4) Still Generating Version 1 Envelope

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I'm trying to codesign an app package that will obey the GateKeeper changes in 10.9.5 and 10.10. The documentation I've seen states that you must codesign on a 10.9 system in order to create a Version 2 envelope.

However, my 10.9.4 system is generating a codesign with a Version 1 envelope. Has anybody else seen this? I've tried reinstalling the xcode developer tools to no avail.

On 10.9.4 my app passes the GateKeeper check:

spctl -a -t exec -vv AppName.app/
AppName.app/: accepted
source=Developer ID
origin=Developer ID Application: Our Company, Inc.

On 10.10 things aren't happy:

spctl -a -t exec -vv AppName.app/
AppName.app/: rejected
AppName.app/: rejected
source=obsolete resource envelope
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Im finding that my call to codesign that worked on 10.9.4 does not work when run on 10.9.5 more details at How do I change how I sign Java application after updating to OSX 10.9.5

It doesn't like something within the bundled jdk, no idea what though.