Maybe this'll fix it...
Apple support docStrictly out of curiosity, have a look at what this contains:
/Users/user_name/Library/Caches/com.apple.helpui
But don't trash anything in Caches, I don't know if the OS will rebuild that directory.
Many help files can be found here:
/Library/Documentation/Help (on the root level)
/Users/user_name/Library/Documentation/ (user's home directory)
That may be the problem, applications seem to install help files in various locations based on the developer's whim.
I've been lucky, I have no problems with the Help Viewer, but there are many others with the same issues as you.