Based on your description, I can only speculate. If you have documented multiple assemblies and produced multiple help files containing one or more of the same assemblies as documentation sources, then each of those help files will contain duplicate topics with duplicate IDs. As such, you will see odd behavior from MS Help Viewer as it's probably showing all of the duplicate topics. If such is the case, the solution would be to factor the common assemblies out into their own help file and add them as reference assemblies to the other projects that need them. In order to produce links to topics in the reference assemblies, you'd need to use the Additional Reference Links plug-in too.
If the above is not the case, in order to properly diagnose the problem I need an example that I can build. If you can e-mail me one, I''ll look into the issue. My e-mail address is in the About box in the standalone GUI and in the footer of the pages in the help file.
Eric