Hi there,
Make sure Captivate 6 is updated to Captivate 6.0.1.240 or Captivate 6.1.0.319 (help > about Adobe Captivate).
Can you tell me which LMS are you using?
Can you test the same course on Scorm Cloud, and check whether you get the proper reporting there?
Also, can you change (just to test) data to report in Points instead of percentage and check whether that makes any difference.
Thanks.