TOC not checking off

Be sure those slides that are not being marked are actually being completed. For example, click spots can extend the timeline beyond the click...so if a click response moves to a new slide, but the timeline for that slide extends beyond the click...that slide may not be 'complete'...

The usual reason for this is that the slides you are showing on the TOC are not ALL the slides in the project, and there are slides AFTER the ones that you don't see get checked off which are NOT shown in the TOC. Captivate thinks these slides must be visited as well otherwise that little group of slides hasn't been completed to its satisfaction.

So what you may need to do is force Captivate to regard the unvisited slides as visited.

In SWF content you can do this with the TicTOC widget from Infosemantics:

About TickTOC AS3 Widget | Infosemantics Pty Ltd

For HTML5 content you'll need be an expert JavaScript programmer, or you can use the CpExtra widget:

Other | Infosemantics Pty Ltd