OK, this has been driving me crazy as well, but not as much noticeable because I was on zerolemon battery. Now I switched back to stock, and it really is draining more battery than usual with exactly the same optimized stock setting I have.
Here is what I did to "fix" that. Click Menu -> Manage Apps -> Running tab. After 4.1.2 update there is a least half a dozen of new background services running in there that come up every time you reboot the phone. Go in and close ("stop") whatever doesn't look familiar to you. Don't worry, if its something that's required - it will restart again once system calls it in the background. Before I had those running, I saw battery dropping about 2% per hour in idle mode. Now, I had my phone idle (actually I have been checking emails) for the last 3+ hours and it only dropped 2%, and I'm sure it would have been down to 1% if I wouldn't be checking emails. That's how it used to be before. So for sure with a new update we got some new system processes running in the background, chewing up battery life. And these are difficult to pin point because it's not a specific app or app setting.
Just keep in mind, once you reboot your phone - everything will be back up and you will have to go back and stop it manually.