At home, SQLExplorer was at least saving connections, but not filters on them. At work it wasn't even doing that (which caused a bit of a grr moment when all my connections vanished after shutdown). The attached patch at least fixes the lack of alias saving, possibly the rest of the problems too, I'll see tomorrow. It looks like its something that someone's come across before as dom4j doesn't seem to like trying to add null elements very much. sqlexplorer.dbproduct.AliasManager checks for them but sqlexplorer.dbproduct.Alias doesn't, the patch adds the same helper method and fix to this class.
Code version at home is the cvs head, at work is whatever version comes down from the update manager at the moment.