what I meant here is that depending of the context in which you are trying to pick a files, some repositories might show up or not, and the ones that are showing up might not display all the files.
As I used as an example, if you are trying to add a picture to a Page resource for example, the repository will not display the files which are not images. It would not make sense to display PDFs or ZIPs in that context.
However, when you browse your repository through your Private Files, you should be able to see all the files that a repository give access to. But you might not see all the repositories available depending on permissions, and multiple other reasons.
I understand you are using Moodle 2.2, and I see that quite a few comparison have been made with Moodle 1.9. I am afraid that my knowledge of Moodle prior to version 2.2 is really small, and even though I have mostly worked with Moodle 2.3 which is quite different regarding the repositories.
I try to find some time to have a look at your questions directly in Moodle 2.2 context.