I have similar problems with Roxy. However, she does have anxiety and nervious behaviors so I always seem to blame it on that. First she has the excited pee - which we have really controlled. She also like to mark things ex: everytime I wash the bathroom or kitchen throw rug, Roxy must pee on it. The cycle never ends

- But Roxy will also run to her box to pee a tiny drop when she is under stress. ex: I am leaving (during weekend time).
Roxy also has the cycle of peeing and not peeing. There are a few months when she only pees in her box. Then there are times when she will contantly pee in the box and on all the thorw rugs and even on the tile. Most instances it's only a little bit and she is 'purposly' doing b/c she is in her pee position.
I too have brought in samples and everything is ok. So being that I know Roxy does have some behavioral issues, I have to say that is what it is all about.
I hope you can get to the bottom of it