I have this problem too! We had a white rug with a yellow flower on it in front of our kitchen sink, untile we notice the yellow flower seemed to be sprouting extra yellow petals lol. We got rid of that one. Now she pees all over the carpet in the basement. I never catch her in the act either

She's PRETTY good at pooping on her pad downstairs, she'll use it about 75% of the time, but she rarely pees on it. Her upstairs pad she's great with though.
I am shampooing my carpets this weekend. I'm also at a loss of what to do!