Trying to assist a friend with this problem:
Using the Ubuntu network manager I can successfully connect to the correct wifi network. It is the ONLY configured (wireless) network. However on every boot an unsecured wifi network is connected to (actually it unsuccessfully attempts to connect to the network, leaving a 169.* addr). Connection to the correct wifi network can be achieved again in network manager simply by making any change, then reverting that change (so that the application will attempt to 'apply' those changes, which connects to the network, as those settings were correct from the start). Solutions given on ubuntuforums have been tried and did not work. gconf-editing system->networking->(something) did not work as the system 'folder' does not contain such a 'subfolder'. All configuration files i've been pointed to seem to ONLY reference the correct network.

I've had similar problems since 7.04; I'm now using 8.04. The network-admin tool doesn't seem too useful for anything other than open networks for me.

A quicker work around than changing the settings and returning to the proper settings using network-admin is to issue:
That restarts the connection without having to change the settings. I emphasize this is just another work around, not a solution. Sorry I couldn't be more helpful.

That workaround does not work, as it simply reconnects (that is, tries and fails to, leaving a 169 addr) to the open net.

Sometimes I need to issue this before I bring it back up...
Regardless, its just another way of doing what you already are doing... and not a solution. Perhaps someone else has an idea.