Also, this feature used to work well on ROMs before KL7 ... Titanium is the same, the ROM isn't ... so somehow it's got to be ROM related, I assume.
And I agree, either Titanium will fix it, or no one.
Sorry, I can't help you out there, I don't have a Note.
You can just remove the apks if you don't want them at all, that way you can copy them back if you change your mind in the future.
Or you can use Gemini App Manager (or similar) to prevent apps from autostarting instead. That way they will just sit there on your phone, but not run until you launch them. Therefore not causing partial wakelocks etc.
...unless someone can say that it is now working of course.