When I was running WordPress MU, the Sitewide Tags plugin would properly coordinate the Categories between the main blog and the sub blog.
Thus if you created a series of Categories on the main blog and one of those was Scissors and was assigned Category ID# of 41, you could then create a sub blog that has no categories other than uncategorized, and if you added the category "Scissors" to this brand new subblog the plugin would somehow "check" with the main blog, notice that it was already there, and would then assign it a Category ID# of 41 as well.
The result was that when you checked the clone posts in the main blog which had be grabbed from the subblog, the categories would match.
I find this not to be so with WordPress 3.0 Multi Site.
If Scissors was Category #41 in the Main blog, and then you added it to the sub-blog at a later time, the sub blog might randomly assign it to category #8 or something.
At this point, when you check the clone post on the main blog, the category assigned would be whatever category #8 happened to be on the main blog...might be cat litter or something...but not scissors.
Does anyone know if this is going to be fixed in the future?