Permission Modules are not Created After Upgrade

Hi,
We have tried to add two global permission modules to an already existing app. After adding modules to the manifest.yml, we run forge deploy and we upgraded the app in the site with forge install --upgrade (as we also made some changes in the permissions). However, when we checked Global Permissions page, permission modules were not created. Are we missing some steps or could this be a bug?
Thanks for the help in advance.