Mark, I have never heard of this issue before and honestly I'm not how the two would be related. iControl does go over the same management channel as the GUI, but the two are different clients altogether. I don't know how an iControl connection could be sharing connection state with a web based GUI request. Each use a independent connection and each send their own set of credentials across the wire. What version of LTM are you on and what client toolkit are you using for iControl. Also, what error are you receiving? Is it a connection refusal or an authentication error. I'm stumped on this one...
-Joe
Nimbostratus