Something has changed in her life. I think it is a status thing. The dogs see all the people and dogs in the household as a pack with each having their own rank in the pack and a top dog. Life is much easier if the 2 legged pack members outrank the 4 legged ones. You can learn to play the role of top dog by reading some books or going to a good obedience class. A good obedience class or book is about you being top dog, not about rewarding standard commands with a treat. Start at
http://www.dogsbestfriend.com/.
For some reason, she feels the need to claim the house by relieving herself, showing she can, and you can't stop her. As they reach 3 years old a dog's personality matures. Quite often they challenge their owner for top dog status.
All the top dog stuff needs to be in addition to what your are doing, the crate, carefully watching her, gating off part of the house, etc. Of course, if she has a physical problem such as a bladder infection, no amount of training will fix that. Some antibiotics from the vet will quickly fix it. You may want to ask about spaying her if not already. This could also be leading up to her season.