After installing LR4.1, neither of my Wacom tablets (wired and wireless) were programmable with it. I had to reinstall LR4.0. Now all is well again. Whatever improvements LR4.1 might have created for me, they weren't worth not being able to use my Wacoms.
I dragged LR4.1 to the trash and then re-installed LR4.0. Now the Wacom keys work fine. Wacom's only solution was to upgrade the driver, which I did, but it didn't help. So my choice is either to use LR4.1 without the keys; or to use LR4.0 with the keys.
This is my experience as well. LR4.1 killed all of my LR4.0 Intuos4 programed keys. Have the most recient driver for my tablet. Had to go back to LR4.0 for the tablet to work again. Not sure if it matters, I sure hope it doesn't, but I'm still on Snow Lepard not Lion.