I have been creating multibranch workflow (version 1.11) projects in Linux and Windows Jenkins installations and I have found next issue. When I create a new Item I choose multibranch project, and I set a name. After that I configure the git project and I push save and next message is shown:

This project scans branches in your SCM and generate a job for each of them, but you have no branches configured. Configure the project and then index branches to get started.

But since I have already set a git repo, I went to Status screen and I could see that all my branches with Jenkinsfile file were being processed. So it seems some kind of refresh problem.