Category hierarchy destroyed by cloning

Hi there,

I just used cloner to create a clone of a multisite site and have had a few problems, the main one is that the category hierarchy got screwed up in the cloned site...

What appears to have happened is that the categories got put in alphabetical order such that category id 1 became 'Al's Blog' and Uncategorised became category id 15- this would be fine except that now when I view my categories in the back end most of them dont show up and 'sub categories' dont show up on the front end of my site any more and the default category gets automatically set to 'Als blog' rather than Uncategorised...

Additionally my site uses plugins that attach styles on post id and category id (so that individual categories or posts can be styled), so changing either of these also really screws things up for me, so is there anyway that Cloner could clone a site and keep the post and category ids intact? In fact I'd be interested to know why its a bad idea or impossibility for all ids, for anything really (menus, widgets etc), to be kept intact (assuming this is a bad idea for some reason) since I am sure lots of plugins make references to these things...

Looking forward to your feedback

David