Im having a similar problem. I have two network cards (11g for my personal network, its internal, and 11b for stumbling, it has a pigtail) ... anyhow... when NetStumber is not running, it behaves nicely. It tells me there are networks to connect to (even though I wish I could stop that as well), but it doesnt connect. However, run Netstumbler, and it instantly connects to anything it can find. I have tcp/ip, microsoft client, etc disabled for the stumbling card, so I don't think its going to kill me. But still, I'd perfer not to become associated with networks I don't personally know. I cant seem to change any of the properties for connections on that card once netstumbler is running, until I close it down.
(its an Orinoco silver 11b external, and a broadcom 11g internal)