You've got to be careful here .... the WLSE can "shut down" rogue APs by either sending a disconnect to the client, or dropping the offending switch port.
The problem is that the "rogue" APs could be other businesses nearby; if you shut down all the "rogue" APs you may be killing another business' wireless system.
You can tell the WLSE that a specific "rogue" is known and acceptable, and it will ignore it for the purposes of reporting.
If you APs or antennas are at some altitude (mine are on the fifth & sixth floor), you can pick up other wireless systems from a mile away ... if I tell my system to shut down all rogues, I can be killing systems for quite a distance.
IMHO, It would be a good idea to bring up a wireless "Sniffer" and identify the traffic; if it's truely rogue/malicious traffic, then shut it down .... but if it's a neighbor, just tell the system to ignore it.
The "Sniffer" can also give you a good idea of which channels are least congested and have the least interference so you can make adjustments to your system.
At the least, bring up something like Netstumbler (it's free, runs on Windows) or Kismet (it's also free, runs on *nix).
You can also run some radio scans from the WLSE. I prefer using an external system.
Good Luck
Scott
