Using LANSurveyor I was able to determine the ports on the cisco switch with the particular interface(s) of the node. Since Atlas Map does not automatically connect interfaces on Window Servers to the port on the switch it makes Atlas Map extremely time consuming. Furthermore, these manual connections in AtLas Map only reports if it is up or down if the "Connect Now" does not work.
In addition, in Atlas Map, if a node connects to two switches before connecting to a the core switch, the "Connect Now" does not connect the lines from node --> switch 4 --> switch 3 --> switch 1. Instead, it connects from node --> switch 1. Not cool.
Please implement LANsurveyor to replace AtLas Map.
are you gathering layer-3 information from the switches? if so, try turning it off may help -- SWO is using the IP<>ARP tables for connection rather than the bridging tables.
I had the same problem with routers and switches across our northernwave network where internal management interfaces were being shown as connected to adjacent switches instead of the actual physical interfaces. turning off gathering L3 information from the switches helped 'fix' the autoconnect.
as an aside: I think that reporting bugs works better opening tickets with SW using your support contract.