Try re-setting the permissions for each individual app in the actual install script.
Are they installed in system/app? I am assuming so?
If you know the permissions code number that you want to set for the app you can set it accordingly. If you want to try something just for testing to see if your app will work but not as a permanent proceedure try this:
set_perm(0777, 0777, 0777, "/system/app/your_app_name_here.apk");
This sets specific permissions to that app in particular as totally open, meaning anything can do anything to that app. Once you boot and test the app and see that it works then bring the permissions back on that app to be suitable.
You can also if you are not keen on installing to system partition do this