Kitty problem

I have 2 indoor cats that are  a year apart in age. Princess will be 2 in sept and Dot will be 1 in sept. I got Princess from someone that had kitties at Walmart and she has been a dream cat. I got her when she was 6 weeks old and she only messed in the house 1 time after that she has always gone in the litter box. Right before Princess turned 1 she started to get really agressive. No one liked her she was flat out mean. I figured that since she was here all day alone that she was lonley and needed a friend so in Oct of last year we went on the new kitty search. We called a few of the free kitty adds and settled on a lady that lived in the next town over. When we went to her house she had 3 females left. We fell in love with 2 of them so we brought them home. These kitties were about 6 weeks old and already eating cat food and they were litter trained already. When we got Dot and Dutchess home they fit right in and after a month or so Princess calmed down. She went back to being a lap cat and loviong everyone. Then the peeing started. We kept finding pee spots all over the house. We started watching and noticed that Dutchess was using the litterbox but she would have accidents all over the place. We took her to the vet and unfortunatly she had kidney problems and after weighing our options decided to have her put down. It wsa the best thing as the vet said her kidneys would fail soon w/o surgery and that surgery was no guarantee. Princess and Dot seemed to be upset for a little while but got over it. Fast forward 4 months~~~there has not been any peeing since Dutchess was put down and we thought everything was good. Well it started again. We were not sure which one was doing it so we took both of them to the vet and they both recieved clean bills of health. They use the litter box all the time, trust me I have to clean it!!! But now someone is peeing all over the house, not necessarily in the same spots as before. My question, if there is nothing medically wrong with them, what would cause 2 females to pee out of the litter box. FYI i scoop the litter box daily and we change it completly evry 2-3 weeks. We use feline pine and have from the beginning so it goes a little longer between changes. Is this a behavior problem? The cats have their own room that they freely come and go, we have our 2nd bathroom turned into a cat room, it has a cat door so they come and go as they please. They have plenty of fresh water avaliable, as well as food. What may be causing this and how can I get them to stop. I really do not want my cats outside because there are coyoties in my neighborhood and I am afraid they will get eatin...Please help!