I had this same problem and resetting PRAM or SMC didn't work for me. What did end up working was maybe a little bit "scorched earth", but someone who's tried everything and can't get it to work may find it useful.
After a couple of trips to the apple genius bar, I realized I should try swiping on my guest account. When I did that, it worked perfectly. I had already disabled and deleted BTT and Air Keyboard, two things I thought may have been messing with it.
The Genius had recommended a clean install of Mavericks, which didn't work. He said it may just have to be restored, although predictably whatever was on there screwing it up before would just do it again. So what ended up being the best option was to move files from my Home folder onto an external, delete the user account, and create a new one. Then you just load back all the files, set up iCloud again, and everything should be working fine. This just also means going through and setting all your preferences over again (took me a few hours, and some time here and there with each program when I realized certain preferences had been reset, default window size etc.).
I would say just make sure to deactivate any programs before doing this and making sure you have activation codes. Final Draft needed it again for the new user, but that was really the only one. Photoshop and LR4 were fine.
And also, as your setting up the new user and adding and enabling programs, make sure to check swiping in Safari, so you don't get to the end and realize something along the way messed it up again.
Again, this was a longer process than resetting PRAM or just putting the system to sleep and then waking, but it finally did the trick for me as a Plan Z. And now it's been working flawlessly for the past week with no problems. So if you go into a guest bare bones account, and the swiping is unaffected, then this may be the best solution.
