This highly depends on which Git provider are you using.
If you are using GitHub or Bitbucket Cloud, the list of organisations you can select depends on which organisation have selected during the authentication process of connecting GitHub or Bitbucket Cloud to Jira. To use more than one organisation, you will have to complete the installation process again for any of the new organisation.
If you are using Bitbucket Server, you (your account) must have access to that organisation in order for you to be able to select it. You must also choose OAuth with impersonation during the setup of Application links. Read more here.
If you are using GitLab, this depends on who has completed the initial connection from Jira to GitLab. Behave Pro will be only able to access groups under the GitLab user you are logged in during the initial setup. It is highly recommended that you create a machine used for this connection and give that user access to the repositories you want Behave Pro to have access to.