As i don't have problem with the led, i'm not removing it just yet. I wonder if you have tried it with clean install of CM12? Also i haven't touched any of the led settings in KTweaker.
And yes, KTweaker does seem to have problems with certain features like IO scheduler and voltages to name a few. I'll probably have to contact @ktoonsez
someday for those... currently working on other project, no time for Android for some time.