Have my screen rotation locked but many programs rotate anyway (eg. Nook). Is there anyway to really lock the rotation while running these programs?
As mr_nobody said, many apps override the rotation setting of the N7. You'll find this a lot with games. Some apps let you control this within their own settings. If not, use an app called Ultimate Rotation Control to individually force apps into the orientation you prefer, overriding their specific settings. This is also the app that many N7 users used to allow home screen rotation, before Google implemented it as a native function in a Jelly Bean update.