Gates should update their functionality only when someone's finished editing them, not while he's doing it in the GUI.
Example:
You have a machine that adds functions to a gate; "off", "explode", "on", where "explode" is a useless function to demonstrate this issue.
You want to switch the machine from "off" to "on" in the gate, but to do that, you have to cycle over "explode", which will immediately be active when that slot in the gate is activated for whatever reason.

To solve that problem, make gates only apply changes made in the GUI when it's closed, additionally add a button "apply" to it's GUI to see changes whithout having to close it.

No one seems to have taken ownership of this one yet. Closing for now. Feel free to discuss further on http://mod-buildcraft.com/forums/index.php?board=4.0.

That sounds like an interesting refinement of the current behavior indeed. There's non-trivial implementation required though, as you need to have two states of the gates. In addition, doing that without loosing the ability to see the current status of the gate may be tricky.

mayby some sort of "apply" button or lock