The fact that the topics sync with the TOC when used standalone confirms the help is OK. It is something in the developer's call that is the issue. There is some information in Snippet 1 on my site but I am not sure it will help in this situation.
See www.grainge.org for RoboHelp and Authoring tips
Since you are synchronizing the TOC in WebHelp, you might want to see a demonstration I put together which showcases the RoboHelp WebHelp API for Context Sensitive Help. It's at this address (be sure to allow popups in your browser)
As Peter correctly mentions, a lot of what happens depends on what (among many methods) your developers have chosen to call the help from the application.
Adobe Certified RoboHelp and Adobe Captivate Instructor.
Hopefully my colleagues won't mind my offering one more tidbit here.
There is one other thing to consider as well. When you generate WebHelp by clicking File > Generate Primary Layout, you choose many different settings in the ensuing dialogs. When you click Next > a time or two you reach a dialog allowing you to choose the Speed Optimization setting shown below.
Sometimes we find that if folks choose the option for Local PC or Intranet, the TOC Synchronization will begin working reliably as opposed to failing sometimes. (The default is for Web Site and is likely the way yours is set right now)
The reason for this is because of the way the TOC elements are created using the Web Site speed optimization.
Perhaps try that setting adjustment, generate your output again and see if things improve?