My iPhone, when docked, reacts to the Apple remote. I cannot find the setting to disable the behaviour. Any idea where the setting is?
The answer to your problem is actually in the manual for your Universal Dock. The link is for a recent model. Pairing should be the same for many. Consult the manual for your model if in doubt. Following the instructions in the manual.
The best approach is to pair the dock with a particular remote so that it only responds to a single remote. if you have a spare remote (sounds like you do) then choose one of them and pair it with your dock.
If this is not an option, then you'll need to physically block the infrared receiver on the dock to keep it from "seeing" any remotes.
Yet another option: take the dock out of the situation. Plug your phone in directly via an iPhone cable.