I think you might be onto something.
My family's devices either have 1.6.1-1 or 1.6.2
Neither of them have reported battery issues since me jailbreaking their devices (and they're on iOS 6.1 as well, so when you said you were on 1.6.2 it immediately rung a bell in my head since I JB their devices before the fix and never bothered doing it all over again with iOS 6.1.2 since it's working perfect for them).
On my iPad 3, battery life has been good as far as I can tell. And it's on NCSettings 1.7.1.
Maybe it's an issue specific to iPhone and conflicting with another tweak, or perhaps manifests itself on its own over time as a 'nasty bug'?
Granted I have probably close to 40+ tweaks but battery life for the most part has been EXCELLENT and same as stock believe it or not. I took a huge gamble with Winterboard and Ayecon because I had a terrible experience with performance and battery on iPhone 3G and really stayed away for years for this reason and because I never found any consistent themes I liked until now.
I am going to try NCSettings 1.6.2 and see if it fixes it and report back.
Thanks for the tip!
Also makes sense, because afaik when the dev included LTE toggle support, not long after that he said he and the team are abandoning the project's support and development all together. Also lines up perfectly; maybe including one thing and fixing others caused this nasty bug that seems impossible to track down on its own or rather difficult even with different people's setups.
Can't hurt to try is my theory! I certainly wont be updating any of the 2-3 tweaks my family has installed on their devices, as the config is perfect.
Gonna try this:
http://iwatcher.net/2013/02/17/ncsettings-1-6-2/
Use Safari Download Manager, open with iFile and copy+paste it to the home directory and name it something easy like 'NCSettings.deb' and open Mobile Terminal, type "su" "alpine" "dpkg -i NCSettings.deb" (or the filename.deb, whichever you rename it to be) without quotes, each a separate line followed by hitting enter.
Sorry if people already know this procedure, or I'm being a parrot (I like to share knowledge), but I hope it helps.
Will report back if 1.6.2 fixes it.