When creating a Pull Request off a forked repo residing in your profile, it defaults to upstream Project.

Steps:
1- Create a repo
2- Fork into your profile
3- Browse to your profile. Create a Pull Request off the forked repo.
4- Notice that it will default to master in the upstream project off where it's been forked

However, if you create a Pull Request off a forked repo residing in a project, it defaults to master within that Project/Repo. It should also default to the upstream.

Steps:
1- Create a repo
2- Fork into a Project in your instance
3- Browse to the fork within the repo above. Create a Pull Request off the forked repo
4- Notice that it will default to master within the fork

Pull Requests created on from forks should have a consistent behaviour.