I'd really appreciate an answer to this, but can't afford a bounty (!).
Here we have a very simple GUI: the user just enters a source word and a target word in two text boxes, then presses a button. Then a lot of whirring takes place, and half a second later an answer is shown. The user goes on doing this until bored, then closes the app. Naturally, when the app restarts, the focus should be on the source, and I am hoping there is a neater way of achieving this than the one described. The commenter below has confirmed my feeling that the problem was an artefact of Lion persistence, which is a real nuisance in simple cases like this.
I set an NSTextField as First Responder (using the window's makeFirstResponder) in the awakeFromNib method of a simple 'controller' class, in a simple Cocoa application in Xcode 4.3, running under Lion.
The makeFirstResponder works fine the first time the app is loaded after reboot, but on every rerun the focus is set to the last field accessed. (I had tried connecting the window's initialFirstResponder outlet to the desired NSTextField, but got the same problem).
I fixed it finally by calling an initialisation function from the NSApplication delegate, and putting the makeFirstResponder call there.
The fix is a bit messy - I added a global variable to the controller, and initialised it to self in awakeFromNib.
I add the information that the Cocoa part of the app is simple, but the bulk of it is a mass of STL stuff in .cpp files, ported from Windows.
Deselect the "Restorable" check box in the attributes inspector for your window in IB. Of course, you then won't have the other behaviors you get with a restorable window like remembering its position and size.