The purpose of the colonic transit test is to determine if the sitz markers passs out of your small bowel and colon in a normal amount of time. So it is expected that the markers will come out in your stool. Here's a bit of info on the test from Medscape:
"In this procedure, abdominal radiography is performed a specific number of days (eg, 5 days) after the patient swallows a capsule filled with radiopaque markers.[2,7] In normal controls, most markers are evacuated by day 5. In patients with slow colonic transit, however, more than 20% of markers remain in the colon, usually in an equally scattered pattern.[1,2,7] Retention of markers in a specific area (eg, the rectosigmoid region such as the lower left colon and rectum) with sufficient transit through the remainder of the colon may indicate mechanical obstruction"