I had the same issue. The answer in my case was that the PackageFormatVersion in SSIS/VS was not the same as the one in the deployment wizard! So when I compiled in VS and used the deployment wizard, the scripts did not execute since they compiled in version 6 and the wizard deployed in version 8. But when I deployed from the VS GUI I got version 6, and the scripts worked. You can check packageformatversion in the package script, and check the version on the server. Good luck 🙂