Okay, I had the same problem some of you were having in Borderlands 2 — my mouse wasn’t showing up in the in-game menus and the starting menu.
What’s going on, at least for me, is that it sees I have a game controller plugged in (I use my PS3 controller with the DS3Tool, that allows you to use it as a wireless XBox 360 controller), and it defaults to that.
So the fix is simple — unplug any game controller you have plugged in. Disable it if necessary. Soon as I did that, I was good as gold.
Hope this helps.