I'm using Adium 1.4.1 on Snow Leopard and the 08Nov2010 version of Skype plugin too. What I do as a workaround for the ROOT group bug (ROOTJKSHFOEIZNGIOEOP) is that I start Adium normally and let all my accounts connect, then I just disconnect from the Skype service (File > Disconnect) and the reconnect (File > Connect) and all my contacts, including Skype ones, are placed correctly in their respective groups. Seems to be some race condition of sorts? I don't know, but that is what I do every time I connect, it is tedious but at least it is better than to have all contacts out of order.