Kitty with worms or not, please help?

Sounds like it could be tapeworm. The problem with any fecal test is that it is a sample - a cat can still have parasites, and they might not show up. Most shelters use something called strongid (Pyrantel) to deworm. It's very effective on roundworms and hookworms, but does not kill tapeworms. The only thing that will kill tapeworm is a medication called Drontal. It needs to be given twice, two weeks apart. Ask the shelter about picking some of that up for her.