I'm not a WASD player, I'm actually a QWES player. As such, my "pick up/activate" keybind has moved from the default "E" to "D" now. This is fine except for when trying to pick up a book that I'm currently reading (which is required for several quests so far. What happens is, even though "Q" and "E" are the new page flips the book will NOT go into my inventory on any keybind except "E" (which is now a page flip). So, in order to pick up a quest related book, or ANY book that I want to take, I have to switch keybinds, pick it up, switch back and continue playing.

So, has anyone found a fix for this oversight yet?

It's the same for the favorite button, if you change the shout button to somewhere else the button for favorite will show up as the remapped location, but you still have to push the old button...

The keybinds shown at the bottom of the screen when reading books/crafting/lockpicking, ect are just not updated after you change the keybinds in the options. For example if you changed E to D, then it will still show up that you need to press E to activate something, but you should press D and it will work, no need to change back the keybinds.

You're wrong. Pushing "D" flips the page. The bind to actually take the book while reading never changes and remains "E" even though "E" remaps to a page flip.

E is basically the activate/take button. If you didn't bind THAT button to D, then sure it won't work that way.

I have my shouts binded to F, which was the favorite button before, now i binded the favorite button to Y and the tooltip still shows that F [Favorite], but if i press Y then that favorites the item.

Don't know of a fix, but I have noticed the same problems when changing keys. I use space for pick up/use, and that works for books, but I swapped M2 and W since I like move forward with the right mouse button, and when I want to equip something to my left hand, W doesn't work. I have to change the controls back, set my weapons the way I want them, and then change the controls again. I've said it before, but the key bindings / UI for this game is just so utterly pathetic. Makes me wonder if the ever even tested the controls on the PC.

It doesn't matter about other keybinds. My favorites is "A" and it works. This is specifically targeting the default value to take a book that you are currently reading. That default value is the same one to "activate" reading the book "E". When you change that default value from "E" to "D" the value to take the book that you are currently reading DOES NOT CHANGE. Instead "E" turns in to flipping the page (as it should) but "D" REMAINS a page flipping value as well.

I'm using http://skyrimnexus.com/downloads/file.php?id=88

Not sure if it's what you're looking for, but it helped me out.