TCC and I took Angel to the vet's today to have her ears checked for ear mites or an ear infection, which you can read about here:
http://www.yorkietalk.com/forums/showthread.php?t=45156. We asked about her stool results and whether they could've been a false negative. She said it's possible, and if we wanted to, we could do another test. She said she didn't really think it mattered how long you wait before giving another sample. She said one client gave a sample of their dog's stool the next day after finishing the meds and the test was positive. She said we could take a scoop of stool for 3 days, put it in some solution and keep it in the fridge and then bring all three samples to the vet's office to be tested for a more accurate result. This would help catch any cysts that might remain or pass through. Since Angel's stool is improving, we're holding off on doing this test. If it becomes watery again, then we'll consider it.