Hi Amy,
The URL rewriter exceptions are certainly a problem that you should address, but I would not expect the underlying problem there to affect page management.
Definitely in my case, and in a lot of other cases that I've read about, it was corrupt data that was the cause of persistant problems after the DNN functionality was fixed. Here's a cut down script that you can run yourself in the Host | SQL page to see the data that is being manipulated during page management.
select PortalID, TabID, ParentId, TabName, Level, TabPath
from dbo.Tabs
where left(TabPath,6) <> N'//Host' and left(TabPath,7) <> N'//Admin'
order by PortalID, TabID
Now that you can see the raw data find a page that is not behaving as expected, specifically you need it's TabId. Find the row for the TabId in question. In this row the ParentId value should be the TabId of the parent page, the Level should be 0 for top level pages (i.e. those with no parent defined), 1 for the next level in the page hierarchy, etc. The TabPath should be of the format //TopLevelTabName//NextTabName//YourTabName; specifically, the tab names (without spaces and punctuation) of your tab and all parent tabs up to the top level must be there.
If the data is right then I have no idea what is causing your page management problems. If you can find examples of bad data then throw it back to your SQL guy and ask him to try again :)
Good luck,
Rhys