My setup is: 3 scoop installs, all path-based. One is a generic install for me to mess with so that if I break it horribly it's not a huge deal, I can just nuke the database. One has had layouts and colours changed, and a couple of stories posted. One is new and hasn't been changed yet, but will be as soon as I finish my homework.
I first noticed this when I had only two installs. They both ran fine, but the stock one would take the background colour, header, and (sometimes) rootdir from the modified one, while still using its own stories. When I installed the third one, it just now took a bizarre combination of the layout of the modified one and a black background (which I don't use anywhere), and its own story.
The problems are intermittent; reloading the page will often clear it, leading me to believe that one of the apache child processes is a bit confused over which database it should be looking in. In httpd.conf, I repeated the <Location></Location> sections only for each subsequent install, putting in the appropriate values for path, database name and so on.
