I have conflicts, so I type:
git mergetool
I then get a message saying:
Hit return to start merge resolution tool
>
I realize this is old, but for future googlers, KDiff3 also has an option where if the merge is trivial, it will resolve it silently and never even show a window.
I've had that happen to me in the past, so it might be what's happening for you. I think the option is called 'Auto save and quit on merge without conflicts'.