Couple questions, what Hotfix of version 9? There were some bugs that may address yours, not specifically but a couple Staging issues with pages were fixed in some of the hotfixes.
Next, was this an upgraded instance or a fresh install of 9? If it's an upgrade, one way to rule out code issues possibly is to create a new instance of 9, get it to the same hotfix as your current site, then just try 'swapping' out the file system (just point the new fresh install to your existing database) and see if things work better, that at least will eliminate or show it's something with code.
The next thing to look at is to make sure the roles and permissions are set to the multiple sites, i'm not sure if this would have an affect but it may...
Check your settings as well to make sure these items are logged for staging, there are settings to tell it what to log and what not to log.
Hope that at least helps a little.