Which environment are you running Promotion Management in? You should be running Promotion Management from the 4.1 SP11 environment as there could be version differences.
What are you using for the login to the environments? We have encountered issues where the login to the Source environment needs to have Administrator permissions to read some of the security for the source. We have also found that the promotions work better if you use an Enterprise account, not a third party add in.
I’ve never tried to migrate an Application but my understanding is that you are only migrating configuration settings and maybe security configuration. You aren’t migrating the application itself because that is part of the installation process, not an object to be migrated.