When you generate, try enabling the following option.
Look at your single source layout properties for the WebHelp layout type. (sounds to me as if you are creating WebHelp output.
Ensure you enable the option for "Enable Substring Search". I don't believe it's enabled by default and you specifically have to tell RoboHelp you want it.
Give that a try and see if it changes things.
In that case, try turning OFF the substring search, generate again and see if that makes a difference.