I have also had this dreaded time out during module listing and cache clearing. Support says that the timeout is set at 30 seconds and if the database does not complete the query and send a response before that, it will time out. Has to do with the load balancers. Using a non cloud sites database will skip the problem as the load balancers are only used when cloud sites is waiting for cloud sites database. This is an annoying issue that begs for a new hosting platform for drupal 7 if not addressed.