Well, TBH I was not able to reproduce the problem although I see sometimes one or another complaining about it. I tried to make some tests and on them as I changed one repository permission the change was ready seen by the user. This test was made with a user that reported the problem. The only point to be aware is that before this test, the user renewed its login at the server. Before renewing, the user had a strange view. He was able to see the groups he manages, he was also able to see that he belogs to all that groups he is manager. But going to the repository view, he had his view denied on a repository. And I could see that this repository had one group this user belongs to configured with admin privilege. I believe this issue is related to users that do not use the "remember me" checkbox on login. If they go too long with his session opened in the browser, he might get errors such as these. One point to remember is that hitting the reload button on browser does not have any effect. Just logging out and logging in again makes things right again.
2014-06-06 16:08:08.051 [http-bio-8443-exec-808] WARN sonia.scm.web.filter.PermissionFilter - user xxxx has not enough permissions